RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14505
(1619 letters)
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 1408 bits (3648), Expect = 0.0
Identities = 477/847 (56%), Positives = 615/847 (72%), Gaps = 45/847 (5%)
Query: 5 AKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFV 64
+I + +E+EM +SYLDYAMSVIVGRALPDVRDGLKPVHRR+L+AM+E+ N ++P+
Sbjct: 2 GDRIIPVNIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVHRRILYAMNELGNTPDKPYK 61
Query: 65 KCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTE 124
K AR+VG+ MGKYHPHGD ++YDALVRMAQ FS+R LVDGQGNFGSIDGD AAAMRYTE
Sbjct: 62 KSARIVGDVMGKYHPHGDSAVYDALVRMAQDFSMRYPLVDGQGNFGSIDGDPAAAMRYTE 121
Query: 125 CRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPP 184
R++KI++ELL D+DKET+DF+ NYDG E+EP+VLP R PNLL+NGSSGIAVGMATNIPP
Sbjct: 122 ARMSKIAHELLADIDKETVDFVPNYDGSEQEPTVLPARFPNLLVNGSSGIAVGMATNIPP 181
Query: 185 HNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRA 244
HNL EVID L ++ NP+ +I +L++IIP PDFPT GII G S + + Y TG+G +++RA
Sbjct: 182 HNLGEVIDACLALIDNPDITIEELMEIIPGPDFPTGGIILGRSGIREAYRTGRGSIVMRA 241
Query: 245 KTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIV 304
K IEE R AII+ E+PYQVNK L+EKI++LVKEKK+E IS+LRDESD+ GMRIV
Sbjct: 242 KAEIEEIK--GREAIIVTEIPYQVNKARLIEKIAELVKEKKIEGISDLRDESDRDGMRIV 299
Query: 305 IELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKR 364
IELKR+ +PE+VLN LYK TQLQ +FG+NMLALV+GQPKLLNLKEIL F+ HRKEVI R
Sbjct: 300 IELKRDAVPEVVLNNLYKHTQLQTSFGINMLALVDGQPKLLNLKEILEAFLEHRKEVITR 359
Query: 365 RTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKII 424
RT FELRKA E AHILEGL IAL NID I +IR++ TP EAK ++E
Sbjct: 360 RTRFELRKAEERAHILEGLLIALDNIDEVIALIRASPTPAEAKEGLME------------ 407
Query: 425 GFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIK 484
+ LS+IQAQ IL M LQRLT +E+ KI ++Y+ ++
Sbjct: 408 -----------------------RFGLSEIQAQAILDMRLQRLTGLERDKIEDEYKELLA 444
Query: 485 KVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDM 544
+ DL DIL++ +R++EII +EL IK K+G RR+EII + EDLI +D+
Sbjct: 445 LIADLKDILASPERLLEIIKEELLEIKEKFGDP----RRTEIIEGEGDIDDEDLIPEEDV 500
Query: 545 VITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRL 604
V+TL++ GYIK P+ EYRAQ+RGG+G TK++D++ LF+A+THD +L F+N GR+
Sbjct: 501 VVTLTHGGYIKRTPLDEYRAQRRGGKGVSGAKTKEDDFVEHLFVASTHDTLLFFTNRGRV 560
Query: 605 YWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIV 664
Y LKV++IP+ SR +RG+PI+N+ L+ EKIT ILP+ R+F + Y+F +T G V
Sbjct: 561 YRLKVYEIPEASRTARGRPIVNLLPLEPGEKITAILPV----REFDDDKYLFFATKNGTV 616
Query: 665 KKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVRAMG 724
KKT LS FSN R +GIIA+NL D LIG LTDG DI+L + +GKA+RF E+ VR MG
Sbjct: 617 KKTSLSEFSNIRSNGIIAINLDEGDELIGVRLTDGDDDILLATKNGKAIRFPESDVRPMG 676
Query: 725 RSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISI 784
R+ARGV G++L + +V+++ V Q +LT TENGYGKRT + EY RG KG+I+I
Sbjct: 677 RTARGVRGIKLREGDEVVSMDVVREDSQEILTVTENGYGKRTPVSEYRLQGRGGKGVITI 736
Query: 785 KTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLC 844
K ++NGK+V A V+ EIMLIT G LIRTRVSEI GR+TQGV LI ++ K+
Sbjct: 737 KITEKNGKLVGALPVDDDDEIMLITDSGKLIRTRVSEISITGRNTQGVRLIRLDEGDKVV 796
Query: 845 GVQRLCK 851
V R+ +
Sbjct: 797 SVARVAE 803
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 1120 bits (2899), Expect = 0.0
Identities = 459/845 (54%), Positives = 610/845 (72%), Gaps = 46/845 (5%)
Query: 8 VISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCA 67
++ + +EEEM +SYLDYAMSVIV RALPDVRDGLKPVHRR+L+AM+E+ ++P+ K A
Sbjct: 1 IVPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSA 60
Query: 68 RVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRL 127
R+VG+ MGKYHPHGD +IYD LVRMAQ FSLR LVDGQGNFGSIDGD AAMRYTE RL
Sbjct: 61 RIVGDVMGKYHPHGDSAIYDTLVRMAQDFSLRYPLVDGQGNFGSIDGDPPAAMRYTEARL 120
Query: 128 NKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNL 187
KI+ ELL D+DKET+DF+ NYDG E+EP+VLP+R PNLL+NGSSGIAVGMATNIPPHNL
Sbjct: 121 TKIAEELLRDIDKETVDFVPNYDGSEQEPTVLPSRFPNLLVNGSSGIAVGMATNIPPHNL 180
Query: 188 TEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTH 247
E+ID +L + NP+ SI +L+++IP PDFPT GII G S + Y TG+G ++IRA+
Sbjct: 181 GEIIDALLAYIDNPDISIQELLEVIPGPDFPTGGIILGRSGIRSAYETGRGSIVIRARAE 240
Query: 248 IEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIEL 307
IEE + + R AII+ E+PYQVNK L+EKI++LV+EKK+E IS++RDESD+ G+RIVIEL
Sbjct: 241 IEE-DSKGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESDREGIRIVIEL 299
Query: 308 KRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTI 367
KR+ + E+VLN LYKQTQLQ +FG+NMLALV G PK+LNLKE+L F+ HRK+VI RRTI
Sbjct: 300 KRDAVAEVVLNNLYKQTQLQVSFGINMLALVKGLPKVLNLKELLEAFVEHRKDVITRRTI 359
Query: 368 FELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFN 427
FELRKA E AHILEGL IAL NID I +IR++ +EAK +++E
Sbjct: 360 FELRKAEERAHILEGLLIALDNIDEVIALIRASQNTEEAKTRLVER-------------- 405
Query: 428 KKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVI 487
+ LS+IQAQ IL M LQRLT +E++K+ +Y+ +++ +
Sbjct: 406 ---------------------FSLSEIQAQAILDMRLQRLTGLEREKLQEEYKELLELIA 444
Query: 488 DLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAIN-PSTEDLIASQDMVI 546
DL DIL++ +R++EII +EL IK ++G RR+EI+ + EDLIA +++V+
Sbjct: 445 DLEDILASEERVLEIIREELEEIKEQFGDP----RRTEIVYDESEDIDIEDLIARENVVV 500
Query: 547 TLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYW 606
TLS+ GY+K P+S YR QKRGG+G KD+D+I QL +A+THDY+L F+N G++YW
Sbjct: 501 TLSHNGYVKRVPVSAYRLQKRGGKGVSGADMKDDDFIEQLLVASTHDYLLFFTNRGKVYW 560
Query: 607 LKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKK 666
LKV+QIP+ SR ++GKPI+N+ L+ E+IT IL + ++F Y+F +T G+VKK
Sbjct: 561 LKVYQIPEASRTAKGKPIVNLLPLQPDERITAILSV----KEFDDGLYLFFATKNGVVKK 616
Query: 667 TLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVRAMGRS 726
T L+ FSN R +GIIA+ L + D LI LT G ++ML S +GKAVRF E VR MGR+
Sbjct: 617 TSLTEFSNIRSNGIIAIKLDDGDELISVRLTSGDDEVMLGSKNGKAVRFPEEEVRPMGRA 676
Query: 727 ARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKT 786
ARGV G++L+ + V++LLV + + +L TENGYGKRT I+EY + +RG KG+ SIK
Sbjct: 677 ARGVRGIKLKNEDFVVSLLVVSEE-SYLLIVTENGYGKRTSIEEYRETSRGGKGVKSIKI 735
Query: 787 NKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGV 846
RNG+VV A V+ E+MLIT+ G LIRT V ++ + GR+TQGV LI ++ KL V
Sbjct: 736 TDRNGQVVGAIAVDDDDELMLITSAGKLIRTSVQDVSEQGRNTQGVRLIRLDEDDKLVSV 795
Query: 847 QRLCK 851
++ K
Sbjct: 796 SKVAK 800
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 1041 bits (2694), Expect = 0.0
Identities = 445/854 (52%), Positives = 592/854 (69%), Gaps = 55/854 (6%)
Query: 1 MNQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWN 60
M+ ++E+ I +E+EM +SYLDYAMSVIVGRALPDVRDGLKPV RR+L+AM E+ +
Sbjct: 1 MSDPSEEIEPIDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPD 60
Query: 61 RPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAM 120
+ + K AR+VG+ MGKYHPHGD SIYDALVRMAQ FSLR LVDGQGNFGSIDGD AAAM
Sbjct: 61 KKYKKSARIVGDVMGKYHPHGDSSIYDALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAM 120
Query: 121 RYTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMAT 180
RYTE RL+KI+ ELL D+DK+T+DF+ NYDG EKEP VLP R PNLL+NGSSGIAVGMAT
Sbjct: 121 RYTEARLSKIAEELLEDIDKDTVDFVPNYDGSEKEPEVLPARFPNLLVNGSSGIAVGMAT 180
Query: 181 NIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRV 240
NIPPHNL EVID ++ ++ NP+ +I++L++II PDFPT GII G S + + Y TG+G +
Sbjct: 181 NIPPHNLGEVIDALIALIDNPDATIDELMEIIKGPDFPTGGIIIGRSGIREAYETGRGSI 240
Query: 241 IIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSG 300
+RAK IE+ + R I+I E+PYQVNK L+EKI++LVKEKK+E IS++RDESD+ G
Sbjct: 241 RVRAKAEIED-TKNGREQIVITEIPYQVNKAKLIEKIAELVKEKKIEGISDIRDESDREG 299
Query: 301 MRIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKE 360
+RIVIELKR+ + E+VLN L+K T LQ +F +NMLALVNG+PK+LNLKEIL F+ HR E
Sbjct: 300 IRIVIELKRDAVAEVVLNNLFKLTDLQTSFNVNMLALVNGRPKVLNLKEILSEFLEHRLE 359
Query: 361 VIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDV 420
V+ RRT +EL KA E HILEGL IAL NID I+IIR + EAK +++
Sbjct: 360 VVTRRTEYELNKAEERLHILEGLLIALLNIDEVIEIIRESKDKPEAKEELMAR------- 412
Query: 421 SKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYE 480
+ LS+ QA+ IL + L+RLT +E++KI + +
Sbjct: 413 ----------------------------FGLSEKQAEAILDLRLRRLTGLEEEKIEKELK 444
Query: 481 NVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPS-TEDLI 539
+ K++ DL IL++ +R+++II EL IK K+G RR+EI+ + EDLI
Sbjct: 445 ELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDE----RRTEIVEEEEDEIEDEDLI 500
Query: 540 ASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFS 599
A +D+V+TLS+ GYIK P+ Y AQ+ + K+ D++ +LF ANTHD +L F+
Sbjct: 501 AEEDVVVTLSHKGYIKRVPLKGYEAQR-----VSGLGLKEGDFLERLFEANTHDTLLFFT 555
Query: 600 NYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMST 659
+ GR+Y LKV+++P+GSR SRG+PI+N+ SL+ EKIT +LP+++++ Y+F++T
Sbjct: 556 SKGRVYKLKVYELPEGSRRSRGEPIVNLLSLEKGEKITAVLPVNDDQ-------YLFLAT 608
Query: 660 SLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYD-IMLFSDSGKAVRFNEN 718
G VKKT LS F N R G IA+ L D L+ +LT D I+L + +GKA+RF E+
Sbjct: 609 KKGYVKKTSLSEFKNIRSKGKIAIKLKEGDELVSVSLTSDGDDDILLVTSNGKALRFPES 668
Query: 719 SVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGT 778
VR MGR A+GV G++L++ KV++L V + + +LT TE GYGKRT I EY RG
Sbjct: 669 EVREMGRGAKGVKGIKLKEGDKVVSLSVVEDDEAKLLTVTERGYGKRTKISEYPVTKRGG 728
Query: 779 KGIISIKTNKRN-GKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITV 837
KG+I IK KRN GKVVAA V+ EIMLIT+ G LIRT VSEI GR+TQGV LI +
Sbjct: 729 KGVILIKGTKRNRGKVVAAITVDEDDEIMLITSRGKLIRTAVSEISITGRNTQGVKLINL 788
Query: 838 ENKSKLCGVQRLCK 851
+ K+ V R+ +
Sbjct: 789 DEDEKVVSVARVKE 802
>gnl|CDD|235775 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 843 bits (2181), Expect = 0.0
Identities = 312/566 (55%), Positives = 425/566 (75%), Gaps = 6/566 (1%)
Query: 1056 KMNINQVVNQILDCFATLFKESLLRHDMRSGEVISAEVIGLDRNFVIINADLKSEAFIPI 1115
K Q N + + FA LF+ESL + R G ++ V+ +D+++V+++ LKSE IP+
Sbjct: 1 KEQDAQNQNDMEESFAELFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPL 60
Query: 1116 EEFKNDNGELEVKIGDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIITG 1175
EEFKN+ GELEVK+GD V V +E +E+GFG+T+LSR+KAKRL +W LEKA E+GEI+ G
Sbjct: 61 EEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLSREKAKRLEAWDKLEKAFENGEIVEG 120
Query: 1176 TINGKVKGGLTVLTNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSH 1235
INGKVKGG TV NG++AFLPGS VD+RPV+DT P EGK ++FKVIKLD+KRNN+V+S
Sbjct: 121 VINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVSR 180
Query: 1236 RAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKH 1295
RAV+EE EER++L+E L+EG V+GVVKNITDYGAF+DLGG+DGLLHITDI+W+RV H
Sbjct: 181 RAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNH 240
Query: 1296 PSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDY 1355
PSE++ +G ++ K+LK+D+EK RVSLG+KQLG DPW + +YP G+++ GKVTN+TDY
Sbjct: 241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDY 300
Query: 1356 GAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCK 1415
GAFVE+E+GIEGLVH+SEM W KN PSK+V + VE+M+LEI+EE+RRISLG+KQCK
Sbjct: 301 GAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCK 360
Query: 1416 DNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFK 1475
+NPWE F+ + G+ ++G +K+ITDFG F+GL+G IDGL+HLSD+SW GEE + +K
Sbjct: 361 ENPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYK 420
Query: 1476 KGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQ 1535
KGDE+EA++L +DVEKERISLGIKQLE DPF + + KGS+V G + + +KGA ++
Sbjct: 421 KGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVK-DKGAFVE 479
Query: 1536 LSNEVEGYLRISEEDNKHEK----KLKIGENIDVLTVLIDHKTRYIQLSFKKKEVIKKKK 1591
L + VEG +R SE + LK+G+ ++ + ID K R I LS K + ++K+
Sbjct: 480 LEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKE 539
Query: 1592 LLTSINANTISGTTNLGLILKAELEK 1617
+ N+ + S TT LG +LKA L+
Sbjct: 540 AIAEYNSASDSKTT-LGDLLKAALKG 564
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 760 bits (1964), Expect = 0.0
Identities = 295/806 (36%), Positives = 456/806 (56%), Gaps = 79/806 (9%)
Query: 1 MNQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWN 60
+ + + LEE + + YL YAM VI+ RALPDVRDGLKPV RR+L+AM E+ +
Sbjct: 3 DMSMLEGIEDLPLEEFLEERYLRYAMYVIMDRALPDVRDGLKPVQRRILYAMSELGLTPD 62
Query: 61 RPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAM 120
F K ARVVG+ +GKYHPHGD SIYDA+VRMAQ FS R LVDGQGNFGSIDGD AAAM
Sbjct: 63 AKFKKSARVVGDVLGKYHPHGDSSIYDAMVRMAQDFSYRYPLVDGQGNFGSIDGDPAAAM 122
Query: 121 RYTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMAT 180
RYTE RL+ I+ LL ++D+ T+DF+ N+DG KEP+VLP R PNLL+NG++GIAVGMAT
Sbjct: 123 RYTEARLSPIAELLLEEIDEGTVDFVPNFDGTLKEPTVLPARFPNLLLNGATGIAVGMAT 182
Query: 181 NIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAG-IIYGLSSVHDGYYTGKGR 239
+IPPHNL EVID ++++ NP+ ++ +L++ +P PDFPT G II G + Y TG+G
Sbjct: 183 DIPPHNLREVIDAAIHLIDNPDATLEELMEFVPGPDFPTGGEIITGRDGIRKAYETGRGS 242
Query: 240 VIIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDK- 298
+ +RA+ IE+ R I+I ELPYQV+K L+E+I++L+ KKL I+++RDESD+
Sbjct: 243 IRVRARWEIEDLAG-GRWQIVITELPYQVSKAKLIEQIAELMNAKKLPGIADVRDESDRE 301
Query: 299 SGMRIVIELKRNEI-PEIVLNKLYKQTQLQNTFGMNMLAL-VNGQPKLLNLKEILYYFIL 356
+ +RIVIE K N + PE ++N L+ T L++++ +NM A+ ++G+P++ LKEIL ++
Sbjct: 302 NPVRIVIEPKSNRVDPEALMNHLFATTDLESSYRVNMNAIGLDGRPRVKGLKEILSEWLD 361
Query: 357 HRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWN 416
HR+EV+ RR+ F L K + HILEGL IA NID I+IIR + E K ++
Sbjct: 362 HRREVVTRRSQFRLDKVEKRLHILEGLLIAFLNIDEVIRIIRES---DEPKANLMAR--- 415
Query: 417 LPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKII 476
+ LS+IQA+ IL++ L+RL +E+ +I
Sbjct: 416 --------------------------------FDLSEIQAEAILELRLRRLAKLEEIEIR 443
Query: 477 NKYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEII--LNAINPS 534
+ + + K++ +L IL++ +++ ++I EL K+G RR+ I AI
Sbjct: 444 KEQDELRKEIAELEAILASERKLRKLIKKELKADAKKFGDP----RRTPIEEAEEAIAID 499
Query: 535 TEDLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKA--MMTKDEDWINQLFIANTH 592
E LI + + + LS G+++ G A + K+ D + F A T
Sbjct: 500 EEALIPDEPVTVVLSKKGWVRR----------AKGHSIDASGLSFKEGDSLLFAFEARTT 549
Query: 593 DYILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKN 652
D +L F++ GR+Y L V ++P + G+P+ + L E+I +L +++
Sbjct: 550 DKLLLFTSTGRVYSLPVHELPSARGD--GEPLTGLVDLAPGEEIVHVLAFDPDQK----- 602
Query: 653 NYVFMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKA 712
+ +++S G L + ++G +NL + D ++ + + + +G+
Sbjct: 603 --LLLASSAGYGFVVTLEDLVARTRAGKAVINLKDGDEVLPPVPVEDDDHLAAITSNGRL 660
Query: 713 VRFNENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIK--- 769
+ F + + +G+ +GV + L K + L N + ++ T GKR L
Sbjct: 661 LVFPLSELPELGK-GKGVKLINLPKDDDGLVDLRVLNPEDGLVLLTA---GKRKLKLKPS 716
Query: 770 --EYTKHNRGTKGIISIKTNKRNGKV 793
E + R +G + + KR +
Sbjct: 717 ELEKYRGKRARRGRLLPRGLKRVPRF 742
Score = 62.4 bits (153), Expect = 1e-09
Identities = 35/150 (23%), Positives = 70/150 (46%), Gaps = 10/150 (6%)
Query: 689 DFLIGAALTDGSYDIMLFSDSGKAVRFNEN---SVRAMGRSARGVIGMRLEKKQKVIALL 745
D L+ A + ++LF+ +G+ + S R G G++ L ++++ +L
Sbjct: 538 DSLLFAFEARTTDKLLLFTSTGRVYSLPVHELPSARGDGEPLTGLVD--LAPGEEIVHVL 595
Query: 746 VSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVNRYHEI 805
+ Q +L A+ GYG +++ R K +I++K +V+ V +
Sbjct: 596 AFD-PDQKLLLASSAGYGFVVTLEDLVARTRAGKAVINLKDG---DEVLPPVPVEDDDHL 651
Query: 806 MLITTGGILIRTRVSEIRKMGRSTQGVILI 835
IT+ G L+ +SE+ ++G+ +GV LI
Sbjct: 652 AAITSNGRLLVFPLSELPELGKG-KGVKLI 680
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 633 bits (1635), Expect = 0.0
Identities = 251/479 (52%), Positives = 318/479 (66%), Gaps = 38/479 (7%)
Query: 30 VGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDAL 89
GRALPDVRDGLKPV RR+L+AM + ++P K AR+VG+ GKYHPHGD S+YD +
Sbjct: 1 NGRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKYHPHGDSSLYDTI 60
Query: 90 VRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNY 149
VRMAQ FS L+D QGNFGS DGD AAAMRYTE RL+ I+ LL D+D T+DF+ NY
Sbjct: 61 VRMAQDFSNNIPLLDPQGNFGSRDGDDAAAMRYTETRLSPIARLLLPDIDDPTVDFVPNY 120
Query: 150 DGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLI 209
DG+E EP VLP PNLL+NGSSGIAVGMATNIPPHNL EVID + ++ NPE SI++L+
Sbjct: 121 DGQEVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHNLREVIDALRALIDNPEASIDELM 180
Query: 210 KIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVN 269
+II PDFPT GII G + + + Y TG+GR IIR K IE+ E R I I ELPYQVN
Sbjct: 181 EIIKGPDFPTGGIIEGRAGIREAYETGRGRYIIRGKYEIED--DEGRNTIEITELPYQVN 238
Query: 270 KKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNT 329
K L EKI++LVK+KK+E IS++RDESD+ G+R VIELKR + E+VLN LYK T+LQ T
Sbjct: 239 KAKLKEKIAELVKDKKIEGISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTT 298
Query: 330 FGMNMLALV-NGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALT 388
FG+NM+A NG+PK LNLKEIL F+ HR EV RR +EL KA HILEGL A+
Sbjct: 299 FGINMVAFDPNGRPKKLNLKEILQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAIL 358
Query: 389 NIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDM 448
NID I +IRS+ EAK +IE
Sbjct: 359 NIDEVINLIRSS---DEAKKALIEELEK-------------------------------- 383
Query: 449 YKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIITDEL 507
S+IQA IL M L+RLT +E++K++ + + + ++ DL IL++ +R ++ +EL
Sbjct: 384 LGFSEIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILASEERPKDLWKEEL 442
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure
and biogenesis].
Length = 541
Score = 616 bits (1590), Expect = 0.0
Identities = 280/545 (51%), Positives = 392/545 (71%), Gaps = 10/545 (1%)
Query: 1070 FATLFKESLL-RHDMRSGEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGELEVK 1128
FA LF+ES + G+V+ V+ ++++ V+++ KSE IPI EF N+ E V+
Sbjct: 5 FAELFEESDKSDEEFEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVEDVVQ 64
Query: 1129 IGDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVL 1188
+GD V V + +E+G G+ +LSR KA+R +W LE+A E+GEI+ G I GKVKGGLTV
Sbjct: 65 VGDEVEVLVLRVEDGEGELVLSRRKAERERAWEKLEEAFENGEIVEGKITGKVKGGLTVD 124
Query: 1189 TNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQ 1248
G++AFLPGSLVD+RPV+D P GK ++FK+++LD+KRNNVVLS RAV+EE E+R+
Sbjct: 125 IEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVLEEERSEQRE 184
Query: 1249 KLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDIST 1308
+L+ L+ G V+GVVKNITDYGAF+D+GG+DGLLHI++I+W+RV HPSE++ +G ++
Sbjct: 185 ELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKV 244
Query: 1309 KILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGL 1368
K++ D+E+ RVSL +KQL DPW G+ +YP G ++ GKVTNLTDYGAFVEIE+G+EGL
Sbjct: 245 KVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGKVTNLTDYGAFVEIEEGVEGL 304
Query: 1369 VHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKK 1428
VH+SE+ W KNV PS++V++ VE+ +L+I+ ERRRISLG+KQ K+NPWE F+ H
Sbjct: 305 VHVSEISWTKKNV-PSEVVKVGQEVEVKVLDIDPERRRISLGLKQLKENPWEEFADKHPV 363
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G+ ++G +KSITDFG F+ L+G IDGL+HLSDLSW PGEE + +KKGDE+EA +L++D
Sbjct: 364 GDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEK-YKKGDEVEAKVLAVD 422
Query: 1489 VEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISE 1548
EKERISLGIKQLE P+ + KGS+V G +KS+ +KGA ++L VEG +R+SE
Sbjct: 423 KEKERISLGIKQLEESPWEEFSEKYKKGSVVKGKVKSVK-DKGAFVELGGGVEGLIRLSE 481
Query: 1549 EDNKHEKKLKIGENIDVLTVLIDHKTRYIQLSFKKKEVIKKKKLLTSINANTISGTTNLG 1608
LK+G+ ++ + V ID K R I LS K E ++K+ L S N + ++LG
Sbjct: 482 ---LSRDVLKVGDEVEAVVVSIDKKNRKILLSIKALERKEEKEALESYNKDD---DSSLG 535
Query: 1609 LILKA 1613
IL
Sbjct: 536 DILGN 540
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 582 bits (1504), Expect = 0.0
Identities = 251/492 (51%), Positives = 324/492 (65%), Gaps = 56/492 (11%)
Query: 13 LEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGE 72
+E+ + K YLDY+MSVI GRA+PDVRDGLKPV RR+L+AM + + P VK AR VG+
Sbjct: 3 IEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGVGD 62
Query: 73 TMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSI-DGDSAAAMRYTECRLNKIS 131
MGKYHPHGD S+YD +VRMAQ FS L+DGQGNFGS DGD AAAMRYTE RL+ ++
Sbjct: 63 VMGKYHPHGDSSLYDTIVRMAQDFSNNYPLLDGQGNFGSRLDGDDAAAMRYTETRLSPLA 122
Query: 132 NELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVI 191
LL D+DK+T+DF+ NYDG+E EP+VLP IPNLL+NGSSGIAVGMATNIPPHNL EVI
Sbjct: 123 RLLLPDIDKDTVDFVPNYDGQEIEPTVLPPIIPNLLVNGSSGIAVGMATNIPPHNLREVI 182
Query: 192 DGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEF 251
D V ++ NP+ SI++L+ I PDFPT G I G G+ ++R K IE+
Sbjct: 183 DAVRRLIDNPDASIDELMMIPWGPDFPTGGEIV-----------GPGKYVVRGKIEIED- 230
Query: 252 NRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDES-DKSGMRIVIELKRN 310
I+I ELPYQVN L+EKI++LVK+KK+E I ++RDES D++G+RIVIELKR
Sbjct: 231 ----DNTIVITELPYQVNTADLIEKIAELVKDKKIEGIIDVRDESHDRTGVRIVIELKRG 286
Query: 311 EIPEIVLNKLYKQTQLQNTFGMNMLALV-NGQPKLLNLKEILYYFILHRKEVIKRRTIFE 369
+ E+VLN LYK T+LQ TF +NMLAL NG+PK NLKEIL F+ HR EV RR +
Sbjct: 287 AMAEVVLNGLYKLTKLQTTFSINMLALFDNGRPKKYNLKEILKEFLDHRLEVYTRRKEYL 346
Query: 370 LRKAREY-AHILEGLTIALTNIDNFIQIIRSTSTP-QEAKNKIIESTWNLPDVSKIIGFN 427
L K HILEGL IAL+ ID I +IRS+ +EAK K++E
Sbjct: 347 LGKLEAERLHILEGLFIALSIIDEIIVLIRSSKDLAKEAKEKLMER-------------- 392
Query: 428 KKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVI 487
++LS+IQA IL M L+RLT +E +K+ + + + K++
Sbjct: 393 ---------------------FELSEIQADAILDMRLRRLTKLEVEKLEKELKELEKEIE 431
Query: 488 DLTDILSNSKRI 499
DL IL++ + +
Sbjct: 432 DLEKILASEEWL 443
>gnl|CDD|233102 TIGR00717, rpsA, ribosomal protein S1. This model describes
ribosomal protein S1, RpsA. This protein is found in most
bacterial genomes in a single copy, but is not present in
the Mycoplasmas. It is heterogeneous with respect to the
number of repeats of the S1 RNA binding domain described
by PFAM model pfam00575: six repeats in E. coli and most
other bacteria, four in Bacillus subtilis and some other
species. rpsA is an essential gene in E. coli but not in
B. subtilis. It is associated with the cytidylate kinase
gene cmk in many species, and fused to it in Treponema
pallidum. RpsA is proposed (Medline:97323001) to assist
in mRNA degradation. This model provides trusted hits to
most long form (6 repeat) examples of RpsA. Among
homologs with only four repeats are some to which other
(perhaps secondary) functions have been assigned [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 516
Score = 583 bits (1505), Expect = 0.0
Identities = 269/517 (52%), Positives = 369/517 (71%), Gaps = 7/517 (1%)
Query: 1070 FATLFKESLLRHDMRSGEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGELEVKI 1129
FA L +ESL + R G ++ V+ ++++ V ++ LKSE IP EEF + E++V
Sbjct: 3 FAQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQV-- 60
Query: 1130 GDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLT 1189
GD V V ++ +E+ FG+T+LSR+KA+R W+ LEKA E G I+ G I GKVKGG V
Sbjct: 61 GDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDL 120
Query: 1190 NGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQK 1249
NG++AFLPGS VD++P+KD GKT+ FK+IKLD+KRNN+V+S RA +EE + R++
Sbjct: 121 NGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREE 180
Query: 1250 LIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTK 1309
L+E LKEG VKGVVKNITD+GAF+DLGG+DGLLHITD++W+RVKHPSE + +GQ++ K
Sbjct: 181 LLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVK 240
Query: 1310 ILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLV 1369
++K+D+EK R+SL +KQLG DPW + ++P G ++ G+VTNLTDYG FVEIE+GIEGLV
Sbjct: 241 VIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLV 300
Query: 1370 HISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKG 1429
H+SEM W+ KN PSK+V+ D VE+MIL+I+ ERRR+SLG+KQCK NPWE F H G
Sbjct: 301 HVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVG 360
Query: 1430 EKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDV 1489
+++ G IK ITDFG F+ L+G IDGLIHLSD+SW G E +KKGDEIEA++L++D
Sbjct: 361 DRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDK 420
Query: 1490 EKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISE- 1548
EK+RISLG+KQL +P+ + GS+V G + I + GA ++L VEG +R SE
Sbjct: 421 EKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEI-KDFGAFVELPGGVEGLIRNSEL 479
Query: 1549 ---EDNKHEKKLKIGENIDVLTVLIDHKTRYIQLSFK 1582
D ++K+G+ ++ V ID K R + LS K
Sbjct: 480 SENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
Score = 131 bits (330), Expect = 2e-31
Identities = 95/360 (26%), Positives = 170/360 (47%), Gaps = 36/360 (10%)
Query: 1241 ESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEI 1299
+ EE K ET + G VKG V I F+D+G +G I
Sbjct: 4 AQLLEESLKTEET-RPGSIVKGTVVAINKDTVFVDVGLKSEGR-----IPKEEFLDAPLE 57
Query: 1300 LTIGQDISTKILKYDQEKNRVSLGM-KQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAF 1358
+ +G ++ + + + L K + WI L Y G+ + GK+ G
Sbjct: 58 IQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFI 117
Query: 1359 VEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMK------ 1412
V++ G+E + S++D K + + T++ I++++++R I + +
Sbjct: 118 VDLN-GVEAFLPGSQVD--VKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVSRRAYLEEE 173
Query: 1413 --QCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPG--E 1468
Q ++ EN K+G+ +KG++K+ITDFG F+ L G +DGL+H++D+SW
Sbjct: 174 RSQAREELLENL----KEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSWKRVKHPS 228
Query: 1469 EIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDT 1528
E + K G E++ ++ D EK RISL +KQL DP+ G + G + ++ T
Sbjct: 229 EYV---KVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNL-T 284
Query: 1529 NKGAIIQLSNEVEGYLRISEED----NKHEKK-LKIGENIDVLTVLIDHKTRYIQLSFKK 1583
+ G +++ +EG + +SE N H K +K G+ ++V+ + ID + R + L K+
Sbjct: 285 DYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 568 bits (1467), Expect = 0.0
Identities = 241/478 (50%), Positives = 313/478 (65%), Gaps = 52/478 (10%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
RA+PDVRDGLKPV RR+L+AM ++ ++ + K AR+VG+ MGKYHPHGD SIYDALVR
Sbjct: 1 RAIPDVRDGLKPVQRRILYAMFKLGLNLDKKYKKVARLVGDVMGKYHPHGDASIYDALVR 60
Query: 92 MAQSFSLRCTLVDGQGNFGSI-DGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNYD 150
MAQ F L+DGQGNFGS DGD AAAMRYTE RL+KI+ EL D+DK+T+DF+ NYD
Sbjct: 61 MAQDFVGNIPLLDGQGNFGSRLDGDKAAAMRYTEARLSKIARELFKDIDKDTVDFVPNYD 120
Query: 151 GKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLIK 210
G EKEP+VLP IPNLL+NG+SGIAVGMATNIPPHNL EVID ++ +L PE ++
Sbjct: 121 GSEKEPTVLPPIIPNLLVNGASGIAVGMATNIPPHNLGEVIDALIALLDGPEITLLK--- 177
Query: 211 IIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNK 270
IP PDFPT G I G + + Y TG+G++ +RAK IEE R I+I ELPY V
Sbjct: 178 -IPGPDFPTGGGIIGSGGIREAYKTGRGKITVRAKIEIEE-----RKTIVITELPYGVWT 231
Query: 271 KSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNTF 330
+ L+E I +LVK KK++ S++RDESD+ G+RIVIELKR PE+VLNKLYK+T+LQ++F
Sbjct: 232 EKLIESIEELVKNKKIK-GSDIRDESDR-GVRIVIELKRGANPEVVLNKLYKKTKLQSSF 289
Query: 331 GMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNI 390
N L L +G PK LNLKEIL F+ HR EV KRR + L K E HILEGL AL I
Sbjct: 290 STNNLVLFDGGPKYLNLKEILKEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLKALNKI 349
Query: 391 DNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYK 450
D I++IR + ++AK ++IE +
Sbjct: 350 DFVIEVIRGSIDLKKAKKELIE-------------------------------------E 372
Query: 451 LSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIITDELN 508
LS+IQA +L M L+RLT E +K+ + E + K++ +L IL++ ++ EL+
Sbjct: 373 LSEIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKILAS---EKKLWIKELD 427
>gnl|CDD|233255 TIGR01061, parC_Gpos, DNA topoisomerase IV, A subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 738
Score = 567 bits (1463), Expect = 0.0
Identities = 292/772 (37%), Positives = 441/772 (57%), Gaps = 52/772 (6%)
Query: 13 LEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGE 72
LEE +S+ YA +I RALPD+RDGLKPV RR+L+AM + N +++P+ K AR VGE
Sbjct: 6 LEEVFGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMFQDGNTFDKPYKKSARTVGE 65
Query: 73 TMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISN 132
MGKYHPHGD SIYDA+VRM+Q + TLV+ GN GSIDGD+AAAMRYTE RL+ I++
Sbjct: 66 IMGKYHPHGDSSIYDAMVRMSQDWKNNWTLVEMHGNNGSIDGDNAAAMRYTEARLSLIAS 125
Query: 133 ELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVID 192
ELL D+DK+T+ FI N+D EKEP+VLP PNLLING++GIA G ATNIPPHNL EVID
Sbjct: 126 ELLKDIDKKTVSFIPNFDDSEKEPTVLPALFPNLLINGATGIAAGYATNIPPHNLNEVID 185
Query: 193 GVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFN 252
++Y + +P CS++ L++I+ PDFPT GII G + Y TGKG+ IIRAK IE N
Sbjct: 186 ALIYRIDHPNCSVDKLMEIVKGPDFPTGGIIQGEDGISKAYETGKGKFIIRAKIEIEV-N 244
Query: 253 RENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEI 312
+ I+I E+PY+ NK ++++KI +++ + K+ I +RDESD++G+RI+IELK++
Sbjct: 245 KNGLNQIVITEIPYETNKANIVKKIEEIIFDNKVAGIEEVRDESDRNGIRIIIELKKDAN 304
Query: 313 PEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRK 372
E +LN L+K T LQ + NM+A+ N P + L L +I H EVI R+ +EL K
Sbjct: 305 AEKILNFLFKHTDLQINYNFNMVAIANRTPIQVGLLSYLDAYIKHCHEVIINRSKYELEK 364
Query: 373 AREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYN 432
A + I+EGL A++ ID I++IRS+ +AK +I++
Sbjct: 365 ASKRLEIVEGLIKAISIIDEIIKLIRSSEDKSDAKENLIDN------------------- 405
Query: 433 TISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDI 492
+K ++ QA+ I+ + L RLTN + ++ + + KK+I L I
Sbjct: 406 ----------------FKFTENQAEAIVSLRLYRLTNTDIFELKEEQNELEKKIISLEQI 449
Query: 493 LSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEI--ILNAINPSTEDLIASQDMVITLSN 550
+++ K +++ +L K ++ RRS+I +N I + +LI ++D + ++
Sbjct: 450 IASEKARNKLLKKQLEEYKKQFAQQ----RRSQIEDFINQIKINESELIENEDYYVLITK 505
Query: 551 LGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYWLKVW 610
GYIK + + K G KD+D + IANT D IL F++ G + + V
Sbjct: 506 AGYIKRTSNRSFASSKYTDFGS-----KDDDILFAQTIANTTDQILIFTSLGNIINIPVH 560
Query: 611 QIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKTLLS 670
++ G+ + N + E I + ++ D P + +++ LG+VK+ L+
Sbjct: 561 KLADIRWKDLGEHLSNKITFDENETIVFVGTMNEFDVDQP---ILVLASKLGMVKRIELT 617
Query: 671 NFS-NPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVRAMGRSARG 729
+ + + L ++D LI A L I L SD G A+ F+ N + +G A G
Sbjct: 618 ELNIKRNSKATLCIKLKDKDHLISAFLQQKDKLICLVSDLGYALVFHTNEIPVVGAKAAG 677
Query: 730 VIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGI 781
V GM+L++ +V + ++ + VL T+ G KR I E +R G
Sbjct: 678 VKGMKLKEDDQVKSGVIFEANESLVLL-TQRGSVKRLSISELVVTSRAATGK 728
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 525 bits (1353), Expect = e-165
Identities = 289/704 (41%), Positives = 416/704 (59%), Gaps = 63/704 (8%)
Query: 8 VISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCA 67
+I I LEE M ++YL YA+ V RALPDVRDGLKPVHRR+L+ + + ++P+ K A
Sbjct: 13 IIKIPLEEAMPENYLPYAVEVAKDRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSA 72
Query: 68 RVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRL 127
R+VG+ +GKYHPHGD S+YDA+V +AQ F+ R L+DG GN+GSIDGDSAAAMRYTE RL
Sbjct: 73 RIVGDILGKYHPHGDSSVYDAMVILAQDFTTRMPLIDGHGNWGSIDGDSAAAMRYTEARL 132
Query: 128 NKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNL 187
I+ E+L D+DK+ ++ + NY EKEP VLP R PNLL+NG+ GIAVG+ATNIPPHNL
Sbjct: 133 TPIAMEMLRDIDKDVVNMVDNYSDSEKEPEVLPARYPNLLVNGAFGIAVGLATNIPPHNL 192
Query: 188 TEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTH 247
EVIDG L + N E + +L+ I PD PT GI+ G S+ Y TG+G+V +RAKT
Sbjct: 193 KEVIDGTLAYIDNNEITTKELMNYIKGPDLPTGGILIGKKSLLSAYETGEGKVTLRAKTK 252
Query: 248 IEEFNREN-RTAIIIDELPYQVNKKSLLEKISQLVKEKK----LECISNLRDESDKSGMR 302
IE+ EN R I+I E PY+ NK LL+ IS++ +KK LE IS++RDESD++G+R
Sbjct: 253 IEKL--ENGRLGIVITEFPYRRNKAKLLQTISEMTADKKHSKALENISDIRDESDRNGIR 310
Query: 303 IVIELKRN---EIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRK 359
VIE K++ ++ E VL LYK+T LQ NM+AL +G+P+ + LK +L +++ H+K
Sbjct: 311 AVIEFKKSADEDVAEKVLKYLYKKTDLQCNISFNMVALADGKPETMGLKTMLKHYVEHQK 370
Query: 360 EVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPD 419
EV+ RRT EL A + HI+EG A+ +D I+ IRS+ + ++A +IE
Sbjct: 371 EVVTRRTKKELEIAEKRFHIVEGFIKAIGIMDEIIKTIRSSKSKKDASENLIEK------ 424
Query: 420 VSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKY 479
+ +D QA+ IL++ L RLT +E +Y
Sbjct: 425 -----------------------------FGFTDEQAEAILELMLYRLTGLEIVAFEKEY 455
Query: 480 ENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIIL--NAINPSTED 537
+ + K + LT ILS+ K ++++I EL +K KYG + RR+ II E+
Sbjct: 456 KELEKLIKKLTKILSSEKELLKVIKKELKEVKEKYG----DERRTSIIEDDEKAKIDVEE 511
Query: 538 LIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILC 597
LI +D+VITLSN G+IK P+ Y R + + ++ D+ L +NT D +L
Sbjct: 512 LIVVEDVVITLSNEGFIKRIPLKSY---NRSNSNVEDIEYREGDFNKFLIQSNTKDTLLI 568
Query: 598 FSNYGRLYWLKVWQIPQGSRNSRGK---PIINMFSLKNKEKITVILPLSNNKRDFPKNNY 654
F++ G +Y +K IP+ +G+ II L EKI + + P+ ++
Sbjct: 569 FTDKGNMYQIKGINIPEFKWKEKGERLDEIIKGIDL-ESEKIIEAYSIEDFT---PQKDF 624
Query: 655 VFMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTD 698
+F+ T G +KKT L F + ++A+ L + LI L D
Sbjct: 625 IFI-TDSGGIKKTSLDKF-VTNYTKLMALKLKKGEKLIKVKLVD 666
Score = 72.4 bits (178), Expect = 1e-12
Identities = 50/198 (25%), Positives = 95/198 (47%), Gaps = 15/198 (7%)
Query: 589 ANTHDYILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSL----KNKEKITVILPLSN 644
N+ +L FS+ G++Y + + + +N + + I N+ +L + EKI I+ +
Sbjct: 751 TNSSKNLLIFSDEGKVYKIPAFML----QNIKNEGI-NISALTGDFEKDEKIIKIISIF- 804
Query: 645 NKRDFPKNNYVFMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSY-DI 703
+F ++ ++ + G+VKKTLL+ F S ED L+ + + +I
Sbjct: 805 ---EFEEDLSIYFFSKKGLVKKTLLNEFKGEGNSTQAYKFKHKEDELVNVDIKEHEEKNI 861
Query: 704 MLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQKVI-ALLVSNNQKQSVLTATENGY 762
+L ++ G A+RF +V MG+ A GV G+ L+ + KVI ++ N + + ++
Sbjct: 862 LLITEKGMAIRFKSEAVNPMGKIASGVTGISLKDEDKVIYGSIIDENDTRKIKLKSKAKD 921
Query: 763 GKRTLIKEYTKHNRGTKG 780
IK+ NR +G
Sbjct: 922 KGEIEIKDIKLQNRAGRG 939
Score = 30.5 bits (69), Expect = 8.9
Identities = 39/164 (23%), Positives = 70/164 (42%), Gaps = 33/164 (20%)
Query: 1424 IIHKKGEKIKGIIKSITDFGIFIGLD-GNIDGL--IHLSDLSWTDPGEEIIRNFKKGDEI 1480
I +++G+ K +I+S T + I D GN+ + I++ + W + KG+ +
Sbjct: 546 IEYREGDFNKFLIQSNTKDTLLIFTDKGNMYQIKGINIPEFKWKE----------KGERL 595
Query: 1481 EAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEV 1540
+ II ID+E E+I + P +++ I D G + + TN ++ L
Sbjct: 596 DEIIKGIDLESEKIIEAYSIEDFTPQKDFIFITDSGGIKKTSLDKFVTNYTKLMAL---- 651
Query: 1541 EGYLRISEEDNKHEKKLKIGEN-IDVLTVLIDHKTRYIQLSFKK 1583
KLK GE I V V + ++I++ KK
Sbjct: 652 ---------------KLKKGEKLIKVKLVDRTREEKFIKIKTKK 680
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 448 bits (1153), Expect = e-139
Identities = 245/725 (33%), Positives = 382/725 (52%), Gaps = 77/725 (10%)
Query: 11 ILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVV 70
I L ++YL+Y+M VI+ RALP + DGLKPV RR+++AM E+ N + K AR V
Sbjct: 4 IDLGNFTEEAYLNYSMYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTV 63
Query: 71 GETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDG-DSAAAMRYTECRLNK 129
G+ +GKYHPHGD + Y+A+V MAQ FS R LVDGQGN+G+ D S AAMRYTE RL+K
Sbjct: 64 GDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSK 123
Query: 130 ISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTE 189
IS LL +L + T+DF N+DG EP +LP R+PN+L+NG++GIAVGMAT+IPPHNL E
Sbjct: 124 ISELLLEELGQGTVDFRPNFDGTLLEPVILPARLPNILLNGTTGIAVGMATDIPPHNLHE 183
Query: 190 VIDGVLYVLHNPECSINDLIKIIPAPDFPTAG-IIYGLSSVHDGYYTGKGRVIIRAKTHI 248
+ D LY++ NP+ ++D++ I+ PDFPT II + Y TG+G +RA+
Sbjct: 184 LADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKAEEIRKIYETGRGSFRMRARWKK 243
Query: 249 EEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSG-MRIVIEL 307
E+ I+I LP+Q++K ++E+I+ +K+KKL IS++RDESD +R+VI
Sbjct: 244 EDG------QIVISALPHQISKSKVIEQIAIQMKDKKLPMISDIRDESDHENPIRVVIVP 297
Query: 308 KRNEI-PEIVLNKLYKQTQLQNTF--GMNMLALVNGQPKLLNLKEILYYFILHRKEVIKR 364
+ N + P+IV+ L+ T L+ ++ MNM+ L + P + NL EIL +++ R+ + R
Sbjct: 298 RSNRVDPDIVMEHLFATTDLEKSYRLNMNMIGL-DNVPAVKNLLEILQEWLVFRRNTVIR 356
Query: 365 RTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKII 424
R + L K + HILEGL IA NID I+IIR P K ++E
Sbjct: 357 RLTYRLNKVLQRLHILEGLRIAFLNIDEVIEIIREEDEP---KTILMER----------- 402
Query: 425 GFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIK 484
+KLS IQA+ IL + L+ L +E+ II++ + K
Sbjct: 403 ------------------------FKLSAIQAEAILNLRLRHLAKLEEHAIIDEQSELEK 438
Query: 485 KVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDM 544
+ L IL + + + +++ E+ KYG +++ + S D+I + +
Sbjct: 439 ERAILEKILKSERELNQLVKKEIQADATKYGLARRSSLEEREEAKQV--SEIDMIPKEPV 496
Query: 545 VITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRL 604
I LS +G++ R+ K + K D + ++ ++ + GR
Sbjct: 497 TIILSKMGWV--------RSAKGHDIDLSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRS 548
Query: 605 YWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIV 664
Y L +P +G+P+ L IT IL S N+ + M++ G
Sbjct: 549 YALDPDNLPSA--RGQGEPLTGKLLLPIGATITNILMYSPNQL-------LLMASDAG-- 597
Query: 665 KKTLLSNFSN---PRKSGIIAVNL-SNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSV 720
L NF++ K+G +NL N + + S I +++G+ + F + +
Sbjct: 598 -YGFLCNFNDLIARNKAGKALINLPENASVIAPLPVNGDSDMIAAITEAGRMLVFPIDDL 656
Query: 721 RAMGR 725
+ +
Sbjct: 657 PELSK 661
Score = 33.7 bits (77), Expect = 0.85
Identities = 25/115 (21%), Positives = 50/115 (43%), Gaps = 7/115 (6%)
Query: 744 LLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAA-TLVNRY 802
L+ S NQ +L A++ GYG + N+ K +I++ N V+A +
Sbjct: 582 LMYSPNQL--LLMASDAGYGFLCNFNDLIARNKAGKALINL---PENASVIAPLPVNGDS 636
Query: 803 HEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRLCKITMIKK 857
I IT G ++ + ++ ++ + +G LI + + + G L + + K
Sbjct: 637 DMIAAITEAGRMLVFPIDDLPELSKG-KGNKLIRIPSANAKRGEDGLLDLKIFNK 690
>gnl|CDD|235851 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 344 bits (886), Expect = e-106
Identities = 141/360 (39%), Positives = 232/360 (64%), Gaps = 8/360 (2%)
Query: 1070 FATLFKESLLR-HDMRSGEVISAEVIGLDRNFVIIN-ADLKSEAFIPIEEFKND---NGE 1124
F+ESL ++ G+V++ EV+ ++ V +N K E IPI E ND +
Sbjct: 1 MMEEFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDIN 60
Query: 1125 LEVKIGDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGG 1184
VK+GD + V + +E+G G+ +LS+ + + +W LE+ E GE++ + VKGG
Sbjct: 61 DVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGG 120
Query: 1185 LTVLTNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMG 1244
L V G++ F+P SL+ R V+D + F+GKT++ K+I+LD ++N V+LS RAV+EE
Sbjct: 121 LVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERA 180
Query: 1245 EERQKLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQ 1304
++++L+ +LKEG V+G V +TD+GAF+D+GG+DGL+HI++++ RV+ PSE++++GQ
Sbjct: 181 AKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQ 240
Query: 1305 DISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKG 1364
++ K+L D E R+SL +K PW G+ + P G + G V LTD+GAFVE+ G
Sbjct: 241 EVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPG 300
Query: 1365 IEGLVHISEMDWINKNV-TPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFS 1423
+EGLVHIS++ +K++ TPS++++ V++ +LE+NEE +RISL +K ++ P E
Sbjct: 301 VEGLVHISQIS--HKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEED 358
Score = 174 bits (443), Expect = 3e-47
Identities = 98/304 (32%), Positives = 161/304 (52%), Gaps = 26/304 (8%)
Query: 1213 EGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGA 1272
G ++ V+K++ N++LS R + E + KL E +EG V+ V + G
Sbjct: 65 VGDELEVYVLKVEDGEGNLLLSKRRLEAE---KAWDKLEEKFEEGEVVEVKVTEVVKGGL 121
Query: 1273 FIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQL----- 1327
+D+ G+ G + + I+ R V+ S+ G+ + KI++ D EKNRV L + +
Sbjct: 122 VVDVEGVRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAVVEEER 179
Query: 1328 ---GIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPS 1384
+ L G + G V LTD+GAFV+I G++GLVHISE+ + PS
Sbjct: 180 AAKKEELLSSLK----EGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSH-ERVEKPS 233
Query: 1385 KIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGI 1444
++V + VE+ +L I+ E RISL +K PWE +G+ I+G +K +TDFG
Sbjct: 234 EVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGA 293
Query: 1445 FIGLDGNIDGLIHLSDLSW---TDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQL 1501
F+ + ++GL+H+S +S P E + ++G E++ +L ++ E++RISL IK L
Sbjct: 294 FVEVLPGVEGLVHISQISHKHIATPSEVL----EEGQEVKVKVLEVNEEEKRISLSIKAL 349
Query: 1502 EGDP 1505
E P
Sbjct: 350 EEAP 353
Score = 140 bits (356), Expect = 1e-35
Identities = 98/399 (24%), Positives = 194/399 (48%), Gaps = 39/399 (9%)
Query: 1245 EERQKLIETLKEGCTVKGVVKNITDYGAFIDLGG--IDGLLHITDIAWRRVKHPSEILTI 1302
EE ++ ++ G V G V + D F+++ G ++G++ I++++ ++ ++++ +
Sbjct: 6 EESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKV 65
Query: 1303 GQDISTKILKYDQEKNRVSLGMKQL-GIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEI 1361
G ++ +LK + + + L ++L W L ++ G + KVT + G V++
Sbjct: 66 GDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDV 125
Query: 1362 EKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMK--------Q 1413
E G+ G + S + + V T+E+ I+E++ E+ R+ L +
Sbjct: 126 E-GVRGFIPASLIS--TRFVEDFS-DFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAA 181
Query: 1414 CKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWT---DPGEEI 1470
K+ + K+G+ ++G + +TDFG F+ + G +DGL+H+S+LS P E+
Sbjct: 182 KKEELLSSL----KEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKP-SEV 235
Query: 1471 IRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNK 1530
G E+E +LSID E ERISL +K P+ +G ++ G +K + T+
Sbjct: 236 ---VSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRL-TDF 291
Query: 1531 GAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVL-IDHKTRYIQLSFKK-- 1583
GA +++ VEG + IS+ +KH L+ G+ + V VL ++ + + I LS K
Sbjct: 292 GAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKV-KVLEVNEEEKRISLSIKALE 350
Query: 1584 ---KEVIKKKKLLTSINANTISGTTNLGLILKAELEKIK 1619
E +++ +LG ++ +L+K+K
Sbjct: 351 EAPAEEEDRREEYRQYELPEEETGFSLGDLIGDKLKKLK 389
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal protein
S1; Provisional.
Length = 863
Score = 351 bits (902), Expect = e-103
Identities = 240/804 (29%), Positives = 381/804 (47%), Gaps = 96/804 (11%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAI------------------ 902
+I +DGP SGK +V +L+AS+LG L++G+ YR TL+A+
Sbjct: 36 IIALDGPAGSGKSSVCRLLASRLGAQCLNTGSFYRAFTLAALRRVSELAVQACSPSPDPD 95
Query: 903 -----------------------NNNIQLDNELELVILIKKLNYNFLGKEVYLNGVNVTT 939
+ L +E V + + ++ +Y+ NV +
Sbjct: 96 AAVGCAAVPHATNLDTSYAPLTAQKKVALFDEAYWVSFARTVALSYRAGVMYVGEENVES 155
Query: 940 LIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKF---PGLVADGRDMGTTVFPDAFLKIF 996
L+R+++V + S A IR + K R +V +GRD+ T VF DA LK +
Sbjct: 156 LLRSDEVESAVSYFAAMPAIRAIMTG---KIRSAVCGARVVCEGRDLTTVVFVDADLKCY 212
Query: 997 LTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTRNLSPLKCPEQAHLLNTSK 1056
L A I+ R RR+ Q + +S +L + RD D+ R + L+C A ++TS
Sbjct: 213 LDASIEARVARRWAQGTSR---LSKQELEQRMRARDAHDRARTVGGLRCAPDALYVDTSC 269
Query: 1057 MNINQVVNQI-----------------------LDCFATLFKESLLRHDMRSGEVISAEV 1093
+ I +V +I +E G V V
Sbjct: 270 LTIEEVCERIAREAHRRALWGGERSVENQEGKGTPLVPRQLQERYSFEAPEPGSVRMGTV 329
Query: 1094 IGLDRNFVIINADLKSEAFIPIEEFKNDNGELEVKIGDFVSVAIESLENGFGDTILSRDK 1153
+ ++ V ++ KSE +P+EEF E K GD V V +E + +G LS+ K
Sbjct: 330 VQVNAGTVFVDIGGKSEGRVPVEEF-----EAPPKAGDGVRVYVERV-TPYGPE-LSKTK 382
Query: 1154 AKRLASWLSLEKAMESGEIITGTIN--GKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTT 1210
A RL + L A G + G I + K G V L G+ AFLP S D + V
Sbjct: 383 ADRLGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPE 442
Query: 1211 PFEGKTMDFKVIKLD-----RKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVK 1265
G T F + ++ R +N+V++ R +EE + R++ ++ +V GVVK
Sbjct: 443 SLIGLTSKFYIERISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVK 502
Query: 1266 NITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMK 1325
+ T +GAFIDLGG DGLLH+ D++W V P E + GQ I K+++ DQ + R++L +K
Sbjct: 503 SFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK 562
Query: 1326 QLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSK 1385
DPW+ ++ + G+VT + D+GAF+E+ +GIEGL HISE W+ K PS
Sbjct: 563 HFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSD 622
Query: 1386 IVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIF 1445
+V++ D VE MIL + + R+SLG+KQ NPWE + G + I +T+ G F
Sbjct: 623 MVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAF 682
Query: 1446 IGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDP 1505
I ++ IDG +H+ DLSW + G EIE +++ D + RI LG+KQL +P
Sbjct: 683 IEMEEGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVKQLSDNP 742
Query: 1506 FNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLR----ISEED---NKHEKKLK 1558
+ + N GS V G + S+ T+ G +++ VEG +R + D + +K
Sbjct: 743 WQVFANAYGVGSTVEGEVSSV-TDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYA 801
Query: 1559 IGENIDVLTVLIDHKTRYIQLSFK 1582
+G+ + + V ++ K R + S +
Sbjct: 802 VGDRVKAVIVDMNVKDRKVAFSVR 825
Score = 212 bits (541), Expect = 2e-56
Identities = 107/321 (33%), Positives = 191/321 (59%), Gaps = 17/321 (5%)
Query: 1213 EGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGA 1272
+G+T++ KVI+LD+ + LS + + E K VKG V I D+GA
Sbjct: 539 KGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKF----GVNDVVKGRVTKIADFGA 594
Query: 1273 FIDLG-GIDGLLHITDIAW-RRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGID 1330
FI+L GI+GL HI++ +W ++ PS+++ IG ++ IL YD + RVSLG+KQ+ +
Sbjct: 595 FIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654
Query: 1331 PWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLN 1390
PW + RYP G R ++ +T+ GAF+E+E+GI+G +H+ ++ W+ + +++
Sbjct: 655 PWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELEVG 714
Query: 1391 DTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDG 1450
+E M++E + + RRI LG+KQ DNPW+ F+ + G ++G + S+TDFGIF+ + G
Sbjct: 715 KEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPG 774
Query: 1451 NIDGLI---HLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGI----KQLEG 1503
++GL+ HL + DPGE + R + GD ++A+I+ ++V+ +++ + ++++
Sbjct: 775 GVEGLVRKQHLVENRDGDPGEAL-RKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQR 833
Query: 1504 DPFNNYVNI---NDKGSLVNG 1521
D + Y++ D+GS G
Sbjct: 834 DELSRYMSAPRGEDEGSFTLG 854
>gnl|CDD|234623 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 329 bits (847), Expect = 6e-98
Identities = 134/350 (38%), Positives = 224/350 (64%), Gaps = 5/350 (1%)
Query: 1073 LFKESLLRHDMRSGEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGEL---EVKI 1129
L + L +R G+++ V+ ++ N V ++ KSE IP+ E D VK+
Sbjct: 290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKV 349
Query: 1130 GDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLT 1189
GD + V + LE+ G +LS+ +A R +W LE+A E+GE + G + VKGGL V
Sbjct: 350 GDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDY 409
Query: 1190 NGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRN-NVVLSHRAVIEESMGEERQ 1248
G++AFLP S V++ V+D + ++G+ ++ K+I+ +RKR VVLS +A++EE ++++
Sbjct: 410 GGVRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKE 469
Query: 1249 KLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDIST 1308
+ +L+EG V+G VK +TD+GAF+D+GG+DGLLH+++I+W RV+ PS++L +G +I
Sbjct: 470 ETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKV 529
Query: 1309 KILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGL 1368
IL D+E ++SL +K+L DPW + +YP G+ +LGKV + +GAFVE+E G++GL
Sbjct: 530 YILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGL 589
Query: 1369 VHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNP 1418
VHIS++ W + P ++ + V+ ILE++ E +RI L +K+ ++ P
Sbjct: 590 VHISQISW-KRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638
Score = 172 bits (437), Expect = 2e-44
Identities = 107/363 (29%), Positives = 193/363 (53%), Gaps = 28/363 (7%)
Query: 1157 LASWLSLEKAMESGEIITGTINGKVKGGLTVLTNGLK-AFLPGSLVDIRPVKDTTPF--E 1213
L LEK + G+I+ GT+ + + V +P + + +
Sbjct: 290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKV 349
Query: 1214 GKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAF 1273
G ++ KV+KL+ + VVLS + E + ++L E + G VKG VK + G
Sbjct: 350 GDEIEVKVLKLEDEDGYVVLSKKEADRE---KAWKELEEAFENGEPVKGKVKEVVKGGLL 406
Query: 1274 IDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNR-VSLGMKQLGIDP- 1331
+D GG+ L + + V+ SE GQ++ KI+++++++ + V L K + +
Sbjct: 407 VDYGGVRAFLPASHVELGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEK 464
Query: 1332 -------WIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPS 1384
W L G + G+V LTD+GAFV+I G++GL+H+SE+ W + PS
Sbjct: 465 EKKKEETWNSLE----EGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEISW-GRVEKPS 518
Query: 1385 KIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGI 1444
++++ D +++ IL+I++E +++SL +K+ +PWEN + G + G + I FG
Sbjct: 519 DVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGA 578
Query: 1445 FIGLDGNIDGLIHLSDLSWT--DPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLE 1502
F+ L+ +DGL+H+S +SW D E+++ +G+E++A IL +D E++RI L IK++E
Sbjct: 579 FVELEPGVDGLVHISQISWKRIDKPEDVL---SEGEEVKAKILEVDPEEKRIRLSIKEVE 635
Query: 1503 GDP 1505
+P
Sbjct: 636 EEP 638
Score = 151 bits (383), Expect = 2e-37
Identities = 99/375 (26%), Positives = 175/375 (46%), Gaps = 36/375 (9%)
Query: 1239 IEESMGEERQKLIE----TLKEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRV 1293
+EE E+ + + ++ G VKG V ++ + F+D+G +G++ + ++ +
Sbjct: 281 MEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEI 340
Query: 1294 KHPSEILTIGQDISTKILKYDQEKNRVSLGMKQL-GIDPWIGLSFRYPRGTRLLGKVTNL 1352
E + +G +I K+LK + E V L K+ W L + G + GKV +
Sbjct: 341 SSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEV 400
Query: 1353 TDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRR-ISLGM 1411
G V+ G+ + S + +E+ I+E N +RR+ + L
Sbjct: 401 VKGGLLVDY-GGVRAFLPASH---VELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSR 456
Query: 1412 K--------QCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSW 1463
K + K+ W + ++G+ ++G +K +TDFG F+ + G +DGL+H+S++SW
Sbjct: 457 KAILEEEKEKKKEETWNSL----EEGDVVEGEVKRLTDFGAFVDIGG-VDGLLHVSEISW 511
Query: 1464 T---DPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVN 1520
P + K GDEI+ IL ID E +++SL +K+L DP+ N GS+V
Sbjct: 512 GRVEKPSD----VLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPWENVEEKYPVGSIVL 567
Query: 1521 GIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH----EKKLKIGENIDVLTVLIDHKTRY 1576
G + I GA ++L V+G + IS+ K E L GE + + +D + +
Sbjct: 568 GKVVRI-APFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKR 626
Query: 1577 IQLSFKKKEVIKKKK 1591
I+LS K+ E
Sbjct: 627 IRLSIKEVEEEPGDI 641
Score = 33.4 bits (77), Expect = 1.1
Identities = 22/104 (21%), Positives = 46/104 (44%), Gaps = 8/104 (7%)
Query: 1507 NNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISE----EDNKHEKKLKIGEN 1562
I +G +V G + S+ + + + EG + + E E + ++ +K+G+
Sbjct: 295 ELEKQIR-RGDIVKGTVVSV-NENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDE 352
Query: 1563 IDVLTVLIDHKTRYIQLSFKKKEVIKKKKLLTSINAN--TISGT 1604
I+V + ++ + Y+ LS K+ + K K L N + G
Sbjct: 353 IEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGK 396
>gnl|CDD|237516 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 312 bits (800), Expect = 1e-93
Identities = 143/442 (32%), Positives = 236/442 (53%), Gaps = 13/442 (2%)
Query: 1070 FATLFK--ESLLRHDMRSGEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGELEV 1127
FA L + E + ++R G+ I+ VI + + V ++ K + + E + +GEL V
Sbjct: 17 FAELLEAYEGERKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADGELTV 76
Query: 1128 KIGDFVSVAIESLENGFGDTILSRDKAKRLASWLS-LEKAMESGEIITGTINGKVKGGLT 1186
+GD V + + S+ + LS KA + LE+A E+G + G + G KGG
Sbjct: 77 AVGDEVELYVVSVNGQ--EIRLS--KALSGQGGAAMLEEAYENGVPVEGKVTGTCKGGFN 132
Query: 1187 VLTNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEE 1246
V G +AF P S +D+R V+D + G+T F + +++ N+V+S RA++E E
Sbjct: 133 VEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEA 192
Query: 1247 RQKLIETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQD 1305
+ +ET+KEG V+G V + +GAF++L G++G++HI++++W RV+ E +++G
Sbjct: 193 LEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDT 252
Query: 1306 ISTKILKYDQEKN----RVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEI 1361
+ K+L ++ K R+SL +KQ G DPW + R G ++ GKV L +GAFVEI
Sbjct: 253 VRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEI 312
Query: 1362 EKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWEN 1421
GIEGLVH+SEM W + P +V D V + I +I+ +RRISL ++ + +PW +
Sbjct: 313 LPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWAD 372
Query: 1422 FSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIE 1481
+ G + G ++ FG+F+ L + GL+ S +S K GD +
Sbjct: 373 VAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVIS-RAGKPATYEKLKPGDSVT 431
Query: 1482 AIILSIDVEKERISLGIKQLEG 1503
++ ID K +ISL G
Sbjct: 432 LVVEEIDTAKRKISLAPAGAAG 453
Score = 150 bits (381), Expect = 3e-38
Identities = 89/290 (30%), Positives = 141/290 (48%), Gaps = 23/290 (7%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERR- 1405
G VT L +GAFVE+ G+EG+VHISE+ W ++ + V + DTV + +L I ++
Sbjct: 208 GTVTRLAPFGAFVELAPGVEGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGIERAKKG 266
Query: 1406 ---RISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLS 1462
RISL +KQ +PW+ K G+K+ G + + FG F+ + I+GL+H+S++S
Sbjct: 267 KGLRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS 326
Query: 1463 WT----DPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSL 1518
WT P + + GD + I ID K RISL ++ EGDP+ + G+
Sbjct: 327 WTRRVNKPEDVVA----PGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAERFAPGTT 382
Query: 1519 VNGIIKSIDTNKGAIIQLSNEVEGYL---RISEEDNKHE-KKLKIGENIDVLTVLIDHKT 1574
V G ++ G + L+ V G L IS +KLK G+++ ++ ID
Sbjct: 383 VTGTVEKRAQF-GLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAK 441
Query: 1575 RYIQLSFKKKEVIKK-----KKLLTSINANTISGTTNLGLILKAELEKIK 1619
R I L+ K+ +A G +LG L+ ++K K
Sbjct: 442 RKISLAPAGAAGSGADDDDWKQFAPKKSAPASGGLGSLGQALQEAMKKKK 491
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 299 bits (769), Expect = 5e-93
Identities = 109/213 (51%), Positives = 144/213 (67%), Gaps = 4/213 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
VI IDGP SGKGTVA+++A KLGFHYLD+GA+YR V L+A+ + + L++E LV L
Sbjct: 5 IVIAIDGPAGSGKGTVAKILAKKLGFHYLDTGAMYRAVALAALRHGVDLEDEEALVALAA 64
Query: 920 KLNYNFLGK----EVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ +F V+LNG +VT IR E+V N ASK+A +R+ L + Q F + PG
Sbjct: 65 HLDISFESDPGGQRVFLNGEDVTDEIRTEEVGNAASKVAAIPEVREALVERQRAFAREPG 124
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
LV DGRD+GT VFPDA LKIFLTA ++R +RRYK+L KG SV DLL + +RD RD
Sbjct: 125 LVMDGRDIGTVVFPDAELKIFLTASAEERAERRYKELQAKGISVDFEDLLAEIKERDERD 184
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
R ++PLK E A LL+TS ++I +VV +IL
Sbjct: 185 SNRAVAPLKPAEDALLLDTSGLSIEEVVEKILA 217
>gnl|CDD|236126 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 280 bits (718), Expect = 1e-82
Identities = 137/332 (41%), Positives = 222/332 (66%), Gaps = 7/332 (2%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEF--KNDNGELE-VKIGDFVSVAIESLEN 1142
G+++ V+ +DR+ V+++ K+E IP E K+D E V++GD V + E+
Sbjct: 36 GDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKED 95
Query: 1143 GFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLTNGLKAFLPGSLVD 1202
G ILS+ +A+ +W ++EK E ++TGT+ VKGGL +L GL+ FLP SLV+
Sbjct: 96 KEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGL-ILDIGLRGFLPASLVE 154
Query: 1203 IRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKG 1262
+R V+D P+ G+ ++ K+I+LD+ RNNVVLS RA +E++ E R + + L++G KG
Sbjct: 155 MRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKG 214
Query: 1263 VVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSL 1322
VV +I ++GAF+DLGG+DGL+H+++++W+ + HPSE++ +GQ+++ ++L D ++ RVSL
Sbjct: 215 VVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSL 274
Query: 1323 GMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNV- 1381
+K DPW + + G + GKVT L +GAFV +E+GIEGLVHISE+ ++V
Sbjct: 275 SLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISEL--AERHVE 332
Query: 1382 TPSKIVQLNDTVEIMILEINEERRRISLGMKQ 1413
P ++VQ+ D V + +++I+ ERRRISL +KQ
Sbjct: 333 VPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
Score = 130 bits (328), Expect = 2e-31
Identities = 106/356 (29%), Positives = 189/356 (53%), Gaps = 42/356 (11%)
Query: 1165 KAMESGEIITGTINGKVKGGLTVLTNGLK--AFLPGSLVDIRPVKDTTPFE----GKTMD 1218
K G+I+ GT+ KV +L G K +P + I+ D P E G ++
Sbjct: 31 KYFNDGDIVEGTVV-KVDRDEVLLDIGYKTEGVIPSRELSIK--HDVDPNEVVEVGDEVE 87
Query: 1219 FKVIKLDRKRNNVVLSH-RAVIEESMGEERQKLIETLKEG-CTVKGVVKNITDYGAFIDL 1276
V++ + K ++LS RA E + G IE +KE V G V + G +D+
Sbjct: 88 ALVLQKEDKEGRLILSKKRAQYERAWGT-----IEKIKEKDGVVTGTVIEVVKGGLILDI 142
Query: 1277 GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLS 1336
G + G L + + RRV+ IGQ+I KI++ D+ +N V L + W+ +
Sbjct: 143 G-LRGFLPASLVEMRRVRDLQPY--IGQEIEAKIIELDKNRNNVVLSRRA-----WLEQT 194
Query: 1337 FRYPRGTRL--LGK-------VTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKI 1386
R L L K V+++ ++GAFV++ G++GLVH+SE+ W K++ PS++
Sbjct: 195 QSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSW--KHIDHPSEV 251
Query: 1387 VQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFI 1446
V++ V + +L+++ +R R+SL +K +++PW+ F+ H G+ + G + + FG F+
Sbjct: 252 VEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFV 311
Query: 1447 GLDGNIDGLIHLSDLS--WTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQ 1500
++ I+GL+H+S+L+ + E++ + GDE+ ++ ID+E+ RISL +KQ
Sbjct: 312 RVEEGIEGLVHISELAERHVEVPEQV---VQVGDEVFVKVIDIDLERRRISLSLKQ 364
Score = 90.9 bits (226), Expect = 1e-18
Identities = 53/164 (32%), Positives = 95/164 (57%), Gaps = 13/164 (7%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSW---TDPGEEIIRNFKKGDEIEAI 1483
+KG+ KG++ SI +FG F+ L G +DGL+H+S+LSW P E + + G E+
Sbjct: 207 QKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVV----EVGQEVTVE 261
Query: 1484 ILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGY 1543
+L +D+++ER+SL +K + DP+ + + G +V G + + GA +++ +EG
Sbjct: 262 VLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKL-VPFGAFVRVEEGIEGL 320
Query: 1544 LRISEEDNKH----EKKLKIGENIDVLTVLIDHKTRYIQLSFKK 1583
+ ISE +H E+ +++G+ + V + ID + R I LS K+
Sbjct: 321 VHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 269 bits (689), Expect = 3e-82
Identities = 110/211 (52%), Positives = 149/211 (70%), Gaps = 2/211 (0%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
+I IDGP SGK TVA+++A KLGFHYLD+GA+YR V L+A+ + + LD+E LV L K
Sbjct: 5 IIIAIDGPAGSGKSTVAKILAEKLGFHYLDTGAMYRAVALAALKHGVDLDDEDALVALAK 64
Query: 920 KLNYNFL-GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKF-PGLV 977
+L+ +F+ V+LNG +V+ IR E+V N ASK+A +R+ L K+Q F K PG+V
Sbjct: 65 ELDISFVNDDRVFLNGEDVSEEIRTEEVGNAASKVAAIPEVREALVKLQRAFAKNGPGIV 124
Query: 978 ADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKT 1037
ADGRD+GT VFPDA LKIFLTA ++R +RRYKQL KGFS +LL + +RD RD
Sbjct: 125 ADGRDIGTVVFPDAELKIFLTASPEERAERRYKQLQAKGFSEVFEELLAEIKERDERDSN 184
Query: 1038 RNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
R ++PLK E A LL+TS ++I +VV +IL+
Sbjct: 185 RAVAPLKPAEDALLLDTSSLSIEEVVEKILE 215
>gnl|CDD|237003 PRK11860, PRK11860, bifunctional 3-phosphoshikimate
1-carboxyvinyltransferase/cytidine monophosphate kinase;
Provisional.
Length = 661
Score = 276 bits (707), Expect = 3e-79
Identities = 108/210 (51%), Positives = 141/210 (67%)
Query: 859 IPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILI 918
+PVI IDGPTASGKGTVA VA LG+HYLDSGALYRL L+A+ + LD+E + L
Sbjct: 442 VPVICIDGPTASGKGTVAARVAEALGYHYLDSGALYRLTALAALRAGVALDDEAAIAALA 501
Query: 919 KKLNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVA 978
+ L F G ++L G +VT IR E AS+++ +R L +Q FR+ PGLVA
Sbjct: 502 RGLPVRFEGDRIWLGGEDVTDAIRTEAAGMGASRVSALPAVRAALLALQRSFRRLPGLVA 561
Query: 979 DGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTR 1038
DGRDMGT +FPDA LK+FLTA + R +RRYKQL+ KG S +++DLL +L RD RD R
Sbjct: 562 DGRDMGTVIFPDAALKVFLTASAEARAERRYKQLISKGISANIADLLADLEARDARDTQR 621
Query: 1039 NLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
+++PLK + A LL+ S + I Q V Q+LD
Sbjct: 622 SVAPLKPAQDALLLDNSDLTIEQAVAQVLD 651
>gnl|CDD|236598 PRK09631, PRK09631, DNA topoisomerase IV subunit A; Provisional.
Length = 635
Score = 243 bits (623), Expect = 2e-68
Identities = 161/519 (31%), Positives = 262/519 (50%), Gaps = 84/519 (16%)
Query: 19 KSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYH 78
++L YA VI RA+PDV DGLKPV RR+L ++ EM++ F K A VVG TM KYH
Sbjct: 10 DNFLQYASYVIKDRAIPDVIDGLKPVQRRILHSLFEMHD---GKFHKVANVVGNTM-KYH 65
Query: 79 PHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSI-DGDSAAAMRYTECRLNKISNELLID 137
PHGD SIY+ALV +A + +D QGNFG++ GD A+A RY ECRL ++ E+L
Sbjct: 66 PHGDASIYEALVNLAN----KDLFIDKQGNFGNLFTGDPASAARYIECRLTPLAKEVL-- 119
Query: 138 LDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYV 197
+KE ++ +YDG+ EP LP +IP +LI G+ GIAVGMAT I PHN E++ V
Sbjct: 120 YNKEITEYEPSYDGRNNEPLCLPAKIPVILIQGAEGIAVGMATKILPHNFNEILQAVKSE 179
Query: 198 LHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRT 257
L ++ PDFPT GI+ V + Y G G+V++RAK IE ++
Sbjct: 180 LLGESFAL--------YPDFPTGGIV----DVSE-YADGNGKVLVRAK--IET---KDEK 221
Query: 258 AIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELK--RNEIPEI 315
I+I E+P+ +SL+ I + ++ K++ S +D + + IE+K R
Sbjct: 222 TIVIREIPFGTTTESLIASIEKAARKGKIKISS----INDYTAENVEIEIKLPRGVYASE 277
Query: 316 VLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKARE 375
V+ LY T + + +N+L + + P + + +I+ + H ++V+K E K E
Sbjct: 278 VIEALYAYTDCEVSISVNLLVIKDRYPVIYTVTDIIKFHAEHLQKVLKMELELERAKLLE 337
Query: 376 --YAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNT 433
+A LE + I + + I + S+ ++ + ++ + F ++
Sbjct: 338 KIFAKTLEQIFIE----ERIYKRIETISSEEDVISIVLSE---------LKPFKEELSRD 384
Query: 434 ISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLT------NMEQKKIINKYENVIKKVI 487
+++ +I L LK+P++R++ N ++ +I+NK
Sbjct: 385 VTE-EDIENL----------------LKIPIRRISLFDIDKNQKEIRILNK--------- 418
Query: 488 DLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEI 526
+L + N K I + ++ + KY R++EI
Sbjct: 419 ELKSVEKNLKSIKGYAINFIDKLLAKYSKEYP--RKTEI 455
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation of
cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 217
Score = 227 bits (581), Expect = 5e-68
Identities = 100/212 (47%), Positives = 143/212 (67%), Gaps = 4/212 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
+I IDGP+ +GK TVA+ VA KLG+ YLDSGA+YR + L+A+ N + L +E L LI
Sbjct: 3 MIIAIDGPSGAGKSTVAKAVAEKLGYAYLDSGAMYRAIALAALQNRVDLTSEDALAELIS 62
Query: 920 KLNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ F+ EV+LNG +V+ IR ++V+N ASK+A F +R+ L K Q K G
Sbjct: 63 HLDIRFIPTNGEVEVFLNGEDVSEAIRTQEVANAASKVAVFPKVREALLKRQQALAKNDG 122
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
++ADGRD+GT VFP+A +KIFL A +++R KRRYKQL KG V+ +LL + +RD RD
Sbjct: 123 IIADGRDIGTVVFPNAEVKIFLDASVEERAKRRYKQLQIKGNEVNFEELLAEIKERDDRD 182
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
R ++PLK + A L+TS ++I++VV +IL
Sbjct: 183 SNREVAPLKKADDALYLDTSNLSIDEVVEKIL 214
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 213 bits (545), Expect = 2e-59
Identities = 94/240 (39%), Positives = 137/240 (57%), Gaps = 6/240 (2%)
Query: 844 CGVQRLCKITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAIN 903
CG RL + K P+I IDGP +GK TV + VA KLG YLD+GA+YR VT +
Sbjct: 269 CGSTRLIDNVFLMKRQPIIAIDGPAGAGKSTVTRAVAKKLGLLYLDTGAMYRAVTWLVLQ 328
Query: 904 NNIQLDNELELVILIKKLNYNFL-----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKN 958
I +E L L+ L + V++NG +VT IR+ +V+++ S IA
Sbjct: 329 EGIDPQDEEALAELLSDLKIELKPSSGSPQRVWINGEDVTEAIRSPEVTSSVSAIAAQPA 388
Query: 959 IRKELFKIQVKFRKFPGLVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFS 1018
+R+ L K Q + + GLVA+GRD+GT VFPDA LKIFLTA +++R +RR L +GF
Sbjct: 389 VRQALVKQQQRIGEKGGLVAEGRDIGTHVFPDAELKIFLTASVEERARRRALDLQAQGFP 448
Query: 1019 V-SMSDLLINLIKRDIRDKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILDCFATLFKES 1077
V + L + +RD D TR ++PL+ + A L T ++I +VV++I+D + E
Sbjct: 449 VIDLEQLEAQIAERDRLDSTREIAPLRKADDAIELITDGLSIEEVVDKIIDLYRDRIPEE 508
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 214 bits (548), Expect = 3e-57
Identities = 187/629 (29%), Positives = 299/629 (47%), Gaps = 110/629 (17%)
Query: 21 YLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPH 80
+LDYA VI+ RA+P + DGLKPV RR+L +M EM++ R + K A VVG TM +YHPH
Sbjct: 31 FLDYASYVILERAVPHIEDGLKPVQRRILHSMKEMDD--GR-YNKVANVVGHTM-QYHPH 86
Query: 81 GDVSIYDALVRMAQSFSLRCTLVDGQGNFGSI-DGDSAAAMRYTECRLNKISNELLIDLD 139
GD SI DALV++ Q + L+D QGN+G+I GD AAA RY E RL+K + E++ +
Sbjct: 87 GDASIGDALVQLGQ----KDLLIDTQGNWGNILTGDGAAAPRYIEARLSKFALEVV--FN 140
Query: 140 KETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLH 199
+T ++ +YDG++KEP LP + P LL G+ GIAVG++T I PHN E+ID + L
Sbjct: 141 PKTTEWQLSYDGRKKEPVTLPVKFPLLLAQGAEGIAVGLSTKILPHNFNELIDASIAYLK 200
Query: 200 NPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAI 259
E + PDFPT GII +S+ +DG G+ RV RAK IE+ + +T +
Sbjct: 201 GKEFKL--------YPDFPTGGII-DVSNYNDGERGGRVRV--RAK--IEK--LDKKT-L 244
Query: 260 IIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNK 319
+I E+PY SL++ I + + K++ I + D + + I++ L P+ ++
Sbjct: 245 VITEIPYGTTTSSLIDSILKANDKGKIK-IKKVEDNTAA-DVEILVHLAPGVSPDKTIDA 302
Query: 320 LYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHI 379
LY T + + N +++ +P L + +IL H ++K+ L + E H
Sbjct: 303 LYAFTDCEVSISPNACVIIDNKPHFLGVSDILRRSTDHTVSLLKQELEIRLSELEEQWHF 362
Query: 380 LEGLTIALTNIDNFIQIIRSTSTPQEAKNKI---IESTWNLPDVSKIIG-----FNKKNY 431
+L I FI+ +I IE V + I F K+
Sbjct: 363 A-----SLEKI--FIE------------ERIYKEIEEAETWEAVIEAIDKGLEPFKKQFI 403
Query: 432 NTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTD 491
+++ +D+ +L++I+ + I K + + I + E I +V
Sbjct: 404 REVTE---------DDIVRLTEIKIKRISKFDSDKADEL-----IARLEAEIAEVKH--- 446
Query: 492 ILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMVITLSNL 551
+ + + +K KYG ++ R++EI D I + +V L
Sbjct: 447 ---HLAHLTDYAIAYFTNLKKKYGKGRE--RKTEIR-------NFDTIEATKVVEANQKL 494
Query: 552 GYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDY--ILCFSNYGRLYWLKV 609
Y+ R + G G K KDE ++A+ D ++ F G+ KV
Sbjct: 495 -YVN-------REEGFIGTGLK----KDE------YVADCSDIDDVIVFRRDGKYMVTKV 536
Query: 610 WQIPQGSRNSRGKPIINMFSLKNKEKITV 638
+ GK II++ K +K T+
Sbjct: 537 -----ADKTFVGKDIIHVAVFKKNDKRTI 560
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP as
the preferred phosphoryl donor.
Length = 147
Score = 184 bits (469), Expect = 9e-54
Identities = 77/195 (39%), Positives = 101/195 (51%), Gaps = 48/195 (24%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
+I IDGP SGK TVA+L+A KLG YLD+G
Sbjct: 1 IIAIDGPAGSGKSTVAKLLAKKLGLPYLDTG----------------------------- 31
Query: 921 LNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVADG 980
IR E+V AS++A +RK L + Q + K PG+V +G
Sbjct: 32 -------------------GIRTEEVGKLASEVAAIPEVRKALDERQRELAKKPGIVLEG 72
Query: 981 RDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTRNL 1040
RD+GT VFPDA LKIFLTA + R KRR KQL KG V + ++L +I+RD RD TR +
Sbjct: 73 RDIGTVVFPDADLKIFLTASPEVRAKRRAKQLQAKGEGVDLEEILAEIIERDERDSTRYV 132
Query: 1041 SPLKCPEQAHLLNTS 1055
+PLK E A +++TS
Sbjct: 133 APLKLAEDAIVIDTS 147
>gnl|CDD|170022 PRK09630, PRK09630, DNA topoisomerase IV subunit A; Provisional.
Length = 479
Score = 170 bits (433), Expect = 4e-45
Identities = 110/332 (33%), Positives = 174/332 (52%), Gaps = 31/332 (9%)
Query: 21 YLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPH 80
++ YA VI+ RA+P + DGLKPV RR+L+ + M++ K A + G TM HPH
Sbjct: 12 FMHYASYVILERAIPHILDGLKPVQRRLLWTLFRMDD---GKMHKVANIAGRTMA-LHPH 67
Query: 81 GDVSIYDALVRMAQSFSLRCTLVDGQGNFGS-IDGDSAAAMRYTECRLNKISNELLIDLD 139
GD I +ALV +A + L+D QGNFG+ + GD AA RY E RL+ ++ E+L + D
Sbjct: 68 GDAPIVEALVVLAN----KGYLIDTQGNFGNPLTGDPHAAARYIEARLSPLAKEVLFNTD 123
Query: 140 KETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLH 199
+ F +YDG+EKEP +LP ++P LL++G GIAVGM T I PHN E+++ + +L+
Sbjct: 124 --LMTFHDSYDGREKEPDILPAKLPLLLLHGVDGIAVGMTTKIFPHNFCELLEAQIAILN 181
Query: 200 NPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAI 259
+ ++ PDFP+ G + Y G G + +RA I N +
Sbjct: 182 DQPFTL--------LPDFPSGGTMDA-----SEYQDGLGSITLRASIDI-----INDKTL 223
Query: 260 IIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNK 319
+I E+ ++L+ I K ++ I +++D S I I+L + + +L
Sbjct: 224 LIKEICPSTTTETLIRSIENAAKRGIIK-IDSIQDFSTDLP-HIEIKLPKGIYAKDLLRP 281
Query: 320 LYKQTQLQNTFGMNMLALVNGQPKLLNLKEIL 351
L+ T+ Q A+ +P ++ EIL
Sbjct: 282 LFTHTECQVILTSRPTAIYQNKPVETSISEIL 313
>gnl|CDD|216937 pfam02224, Cytidylate_kin, Cytidylate kinase. Cytidylate kinase
EC:2.7.4.14 catalyzes the phosphorylation of cytidine
5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP)
in the presence of ATP or GTP.
Length = 158
Score = 159 bits (404), Expect = 6e-45
Identities = 65/149 (43%), Positives = 96/149 (64%)
Query: 920 KLNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVAD 979
++ G V+LNG +V+ IR ++V+N AS++A +R L K+Q + K +V +
Sbjct: 10 SFSFRKDGPLVFLNGEDVSEEIRTQEVANAASEVAAIPAVRAILVKLQRQLAKNGNIVME 69
Query: 980 GRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTRN 1039
GRD+GT VFPDA +KIFLTA ++R KRRYKQL KG +V + +LL + +RD RD R
Sbjct: 70 GRDIGTVVFPDAEVKIFLTASPEERAKRRYKQLQAKGSAVDLEELLAEIKRRDKRDSERA 129
Query: 1040 LSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
+ PLK E A ++TS + I +VV +IL+
Sbjct: 130 VGPLKPAEDALYIDTSDLTIEEVVEKILE 158
>gnl|CDD|222896 PHA02592, 52, DNA topisomerase II medium subunit; Provisional.
Length = 439
Score = 152 bits (387), Expect = 2e-39
Identities = 125/490 (25%), Positives = 206/490 (42%), Gaps = 79/490 (16%)
Query: 22 LDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGE-TMGKYHPH 80
L+YAM + RA+P++ DGLKPV R V+ E F K A + G YH H
Sbjct: 17 LEYAMYTVEERAIPNLIDGLKPVQRFVIHRALEYAKGNKEKFDKVAAIAGGVADLGYH-H 75
Query: 81 GDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDK 140
G+ S DA MA +++ L+DGQGNFGS AAA RY R++ ++ D
Sbjct: 76 GETSAQDAGALMANTWNNNIPLLDGQGNFGSRLVQKAAAARYIFARVHDNFRKIYKD--- 132
Query: 141 ETIDFISNYDGKEKEPSV--LPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVL 198
D ++ E P LP IP +L+NG SGIA G ATNI PH+ VI VL L
Sbjct: 133 --EDLAPVHEDPEHIPPAFYLPI-IPMVLLNGVSGIATGYATNILPHSPKSVIKAVLAAL 189
Query: 199 HNPECSINDLIKIIPAPDFPT-AGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRT 257
+ + + P FP G + G IR + +T
Sbjct: 190 NGKDITE-------PKVQFPEFKGEVV---------EIEPGSYEIRGT-----YELNGKT 228
Query: 258 AIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVL 317
+ I E+P + ++++ + + L ++ K I + D+ + G R + LKR E E
Sbjct: 229 KLHITEIPVKYDRETYVAVLDPLEEKGK---IVSY-DDCTEDGFRFKVTLKREENEEATH 284
Query: 318 NKLYKQTQLQNTFGMNMLALV-NGQPKLL-NLKEILYYFILHRKEVIKRRTIFELRKARE 375
K+ K L N+ + NG+ K+ N ++++ F+ RK +++R +E+++ E
Sbjct: 285 EKIMKDFGLIERVSQNITVINENGKLKVYENAEDLIRDFVEIRKTYVQKRIQYEIKETEE 344
Query: 376 YAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTIS 435
+AL AK + I+ V +
Sbjct: 345 ------AFDLAL------------------AKAEFIKRVIAGEIVL----------QGKT 370
Query: 436 KINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSN 495
+ +L +N + A +++ M + +T+ E++K+ + E + K+ +
Sbjct: 371 RSELTEELSDNKDFGE---YADKLVAMNIYSMTSDEREKLQKEAEELEKEH----EYWKK 423
Query: 496 SKRIIEIITD 505
+ E I D
Sbjct: 424 TTAKKEYIKD 433
>gnl|CDD|240194 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1
(RPS1) domain. RPS1 is a component of the small ribosomal
subunit thought to be involved in the recognition and
binding of mRNA's during translation initiation. The
bacterial RPS1 domain architecture consists of 4-6 tandem
S1 domains. In some bacteria, the tandem S1 array is
located C-terminal to a 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase (HMBPP reductase) domain. While
RPS1 is found primarily in bacteria, proteins with tandem
RPS1-like domains have been identified in plants and
humans, however these lack the N-terminal HMBPP reductase
domain. This CD includes S1 repeat 4 (ec4) of the
Escherichia coli RPS1. Autoantibodies to double-stranded
DNA from patients with systemic lupus erythematosus
cross-react with the human RPS1 homolog.
Length = 72
Score = 131 bits (331), Expect = 3e-36
Identities = 54/72 (75%), Positives = 64/72 (88%)
Query: 1339 YPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMIL 1398
YP GTRL GKVTNLTDYG FVE+E+G+EGLVH+SEMDW NKN+ PSK+V L D VE+M+L
Sbjct: 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVL 60
Query: 1399 EINEERRRISLG 1410
+I+EERRRISLG
Sbjct: 61 DIDEERRRISLG 72
Score = 61.1 bits (148), Expect = 1e-11
Identities = 26/72 (36%), Positives = 48/72 (66%)
Query: 1426 HKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
+ +G ++ G + ++TD+G F+ L+ ++GL+H+S++ WT+ + GDE+E ++L
Sbjct: 1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVL 60
Query: 1486 SIDVEKERISLG 1497
ID E+ RISLG
Sbjct: 61 DIDEERRRISLG 72
Score = 60.7 bits (147), Expect = 2e-11
Identities = 27/70 (38%), Positives = 50/70 (71%), Gaps = 2/70 (2%)
Query: 1256 EGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAW-RRVKHPSEILTIGQDISTKILKY 1313
EG + G V N+TDYG F++L G++GL+H++++ W + HPS+++++G ++ +L
Sbjct: 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDI 62
Query: 1314 DQEKNRVSLG 1323
D+E+ R+SLG
Sbjct: 63 DEERRRISLG 72
Score = 32.5 bits (74), Expect = 0.19
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 5/57 (8%)
Query: 1528 TNKGAIIQLSNEVEGYLRISEED----NKHEKKL-KIGENIDVLTVLIDHKTRYIQL 1579
T+ G ++L VEG + +SE D N H K+ +G+ ++V+ + ID + R I L
Sbjct: 15 TDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
>gnl|CDD|240193 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1
(RPS1) domain. RPS1 is a component of the small ribosomal
subunit thought to be involved in the recognition and
binding of mRNA's during translation initiation. The
bacterial RPS1 domain architecture consists of 4-6 tandem
S1 domains. In some bacteria, the tandem S1 array is
located C-terminal to a 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase (HMBPP reductase) domain. While
RPS1 is found primarily in bacteria, proteins with tandem
RPS1-like domains have been identified in plants and
humans, however these lack the N-terminal HMBPP reductase
domain. This CD includes S1 repeat 3 (ec3) of the
Escherichia coli RPS1. Autoantibodies to double-stranded
DNA from patients with systemic lupus erythematosus
cross-react with the human RPS1 homolog.
Length = 68
Score = 120 bits (304), Expect = 1e-32
Identities = 41/68 (60%), Positives = 58/68 (85%)
Query: 1256 EGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
EG V+G VK+ITD+GAF+DLGG+DGLLHI+D++W RVKHPSE++ +G ++ K+LK D+
Sbjct: 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK 60
Query: 1316 EKNRVSLG 1323
E+ R+SLG
Sbjct: 61 ERKRISLG 68
Score = 81.5 bits (202), Expect = 8e-19
Identities = 35/73 (47%), Positives = 49/73 (67%), Gaps = 8/73 (10%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIEAII 1484
+G+ ++G +KSITDFG F+ L G +DGL+H+SD+SW P E GDE+E +
Sbjct: 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEV----VNVGDEVEVKV 55
Query: 1485 LSIDVEKERISLG 1497
L ID E++RISLG
Sbjct: 56 LKIDKERKRISLG 68
Score = 75.0 bits (185), Expect = 2e-16
Identities = 32/69 (46%), Positives = 52/69 (75%), Gaps = 2/69 (2%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
G + G V ++TD+GAFV++ G++GL+HIS+M W + PS++V + D VE+ +L+I+
Sbjct: 2 GDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKID 59
Query: 1402 EERRRISLG 1410
+ER+RISLG
Sbjct: 60 KERKRISLG 68
Score = 33.8 bits (78), Expect = 0.052
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 1515 KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLI 1570
+G +V G +KSI T+ GA + L V+G L IS+ K + +G+ ++V + I
Sbjct: 1 EGDVVEGTVKSI-TDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKI 58
Query: 1571 DHKTRYIQLS 1580
D + + I L
Sbjct: 59 DKERKRISLG 68
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 131 bits (332), Expect = 4e-31
Identities = 62/229 (27%), Positives = 110/229 (48%), Gaps = 27/229 (11%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
++ IDGP GK +V++ +A LG+ YLD+GA+YR + I LD EL ++ +
Sbjct: 3 IVAIDGPAGVGKSSVSRALAQYLGYAYLDTGAMYRACAWWCLKQGIDLDAELVDEQVVTE 62
Query: 921 ------------LNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQV 968
++ + V+ +G +++ IR+ +VS++ S +A +R L Q
Sbjct: 63 AVGEFFTGLHFDISVDPDSPGVFADGEDISEEIRSPEVSSHVSAVAAIPPVRNVLIAAQR 122
Query: 969 K----------FRKFPGLVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFS 1018
F G+VA+GRD+ T V PDA ++I LTA + R RR Q +
Sbjct: 123 AYIAREASADSFSGGLGIVAEGRDITTVVAPDAEVRILLTAREEVRQARRSGQDRSETPG 182
Query: 1019 VSMSDLLINLIKRDIRDKTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
V + D+ RD D ++ S L + L+ S ++ ++ ++ ++
Sbjct: 183 VVLEDVA----ARDEAD-SKVTSFLSAADGVTTLDNSDLDFDETLDLLI 226
>gnl|CDD|240195 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1
(RPS1) domain. RPS1 is a component of the small ribosomal
subunit thought to be involved in the recognition and
binding of mRNA's during translation initiation. The
bacterial RPS1 domain architecture consists of 4-6 tandem
S1 domains. In some bacteria, the tandem S1 array is
located C-terminal to a 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase (HMBPP reductase) domain. While
RPS1 is found primarily in bacteria, proteins with tandem
RPS1-like domains have been identified in plants and
humans, however these lack the N-terminal HMBPP reductase
domain. This CD includes S1 repeat 5 (ec5) of the
Escherichia coli RPS1. Autoantibodies to double-stranded
DNA from patients with systemic lupus erythematosus
cross-react with the human RPS1 homolog.
Length = 69
Score = 112 bits (281), Expect = 2e-29
Identities = 43/69 (62%), Positives = 54/69 (78%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G + G IKSITDFGIF+GLDG IDGL+H+SD+SWT +KKG E+EA++L+ID
Sbjct: 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60
Query: 1489 VEKERISLG 1497
VE+ERISLG
Sbjct: 61 VERERISLG 69
Score = 81.8 bits (202), Expect = 8e-19
Identities = 37/69 (53%), Positives = 51/69 (73%), Gaps = 2/69 (2%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAW-RRVKHPSEILTIGQDISTKILKYD 1314
G V G +K+ITD+G F+ L GGIDGL+HI+DI+W +RV+HPSEI GQ++ +L D
Sbjct: 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60
Query: 1315 QEKNRVSLG 1323
E+ R+SLG
Sbjct: 61 VERERISLG 69
Score = 75.2 bits (185), Expect = 2e-16
Identities = 32/69 (46%), Positives = 48/69 (69%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
GT + GK+ ++TD+G FV ++ GI+GLVHIS++ W + PS+I + VE ++L I+
Sbjct: 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNID 60
Query: 1402 EERRRISLG 1410
ER RISLG
Sbjct: 61 VERERISLG 69
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 117 bits (294), Expect = 2e-28
Identities = 74/250 (29%), Positives = 129/250 (51%), Gaps = 14/250 (5%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEF---KNDNGELEVKIGDFVSVAIESLEN 1142
G++++ V L+ +I+ K+ AF+PI+E + + E ++ + I S EN
Sbjct: 32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDEN 91
Query: 1143 GFGDTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLTNGLKAFLPGSLVD 1202
G LS + + + +W + + + + + +GG V GL+ F+PGS +
Sbjct: 92 EDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHIS 151
Query: 1203 IRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHR-AVIEESMGEERQKLIETLKEGCTVK 1261
R K+ G+ + K +++D +RN +VLSHR A++E M L+ G V
Sbjct: 152 TRKPKEE--LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNR--------LEVGEVVV 201
Query: 1262 GVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVS 1321
G V+ I YGAFID+GG+ GLLHI++I+ ++ P + + ++ I+ D E+ R+S
Sbjct: 202 GTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRIS 261
Query: 1322 LGMKQLGIDP 1331
L KQL +P
Sbjct: 262 LSTKQLEPEP 271
Score = 85.6 bits (212), Expect = 1e-17
Identities = 74/254 (29%), Positives = 134/254 (52%), Gaps = 19/254 (7%)
Query: 1170 GEIITGTI-NGKVKGGLTVLTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMDFKVIKLDR 1226
G+I+ GT+ + + +G L + AF+P + I V+ +T +F ++ +
Sbjct: 32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDEN 91
Query: 1227 KRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHIT 1286
+ + LS R IE ER + ++ KE TV+ V GA + + G+ G + +
Sbjct: 92 EDGQLTLSIRR-IEYMRAWERVRQLQ--KEDATVRSEVFATNRGGALVRIEGLRGFIPGS 148
Query: 1287 DIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLL 1346
I+ R+ K E L +G+++ K L+ D+E+NR+ L ++ ++ + R G ++
Sbjct: 149 HISTRKPK---EEL-VGEELPLKFLEVDEERNRLVLSHRRALVERKMN---RLEVGEVVV 201
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEM--DWINKNVTPSKIVQLNDTVEIMILEINEER 1404
G V + YGAF++I G+ GL+HISE+ + I TP + +ND +++MI++++ ER
Sbjct: 202 GTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIE---TPHSVFNVNDEMKVMIIDLDAER 257
Query: 1405 RRISLGMKQCKDNP 1418
RISL KQ + P
Sbjct: 258 GRISLSTKQLEPEP 271
Score = 68.3 bits (167), Expect = 6e-12
Identities = 75/274 (27%), Positives = 126/274 (45%), Gaps = 55/274 (20%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEILTIGQDISTKILKY 1313
K G V G V ++ GA ID+G + I +++ RV+ P E+L + IL
Sbjct: 30 KPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSD 89
Query: 1314 DQEKNRVSLGMKQLGIDPWIGLSFRYPRG---TRLLGK----------VTNLTDYGAFVE 1360
+ E +++L ++++ Y R R L K TN GA V
Sbjct: 90 ENEDGQLTLSIRRI----------EYMRAWERVRQLQKEDATVRSEVFATNRG--GALVR 137
Query: 1361 IEKGIEGLV---HISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDN 1417
IE G+ G + HIS K + + + + LE++EER R+ L ++
Sbjct: 138 IE-GLRGFIPGSHISTRK--------PKEELVGEELPLKFLEVDEERNRLVLSHRR---- 184
Query: 1418 PWENFSIIHKK------GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEII 1471
+++ +K GE + G ++ I +G FI + G + GL+H+S++S + E
Sbjct: 185 -----ALVERKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEIS-HEHIETPH 237
Query: 1472 RNFKKGDEIEAIILSIDVEKERISLGIKQLEGDP 1505
F DE++ +I+ +D E+ RISL KQLE +P
Sbjct: 238 SVFNVNDEMKVMIIDLDAERGRISLSTKQLEPEP 271
>gnl|CDD|239911 cd04465, S1_RPS1_repeat_ec2_hs2, S1_RPS1_repeat_ec2_hs2: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP
reductase) domain.While RPS1 is found primarily in
bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1
(ec2 and hs2, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 67
Score = 97.1 bits (243), Expect = 3e-24
Identities = 37/67 (55%), Positives = 50/67 (74%)
Query: 1170 GEIITGTINGKVKGGLTVLTNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRN 1229
GEI+ G + KVKGGL V G++AFLP S VD+RPV+D + GK + FK+I++DR+RN
Sbjct: 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERN 60
Query: 1230 NVVLSHR 1236
N+VLS R
Sbjct: 61 NIVLSRR 67
Score = 42.1 bits (100), Expect = 6e-05
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 1259 TVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKN 1318
V+G V G +D+ G+ L + + R V+ E +G+++ KI++ D+E+N
Sbjct: 3 IVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERN 60
Query: 1319 RV 1320
+
Sbjct: 61 NI 62
Score = 28.6 bits (65), Expect = 4.7
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRR 1406
GKVT G V+IE G+ + S++D + V + ++ I+EI+ ER
Sbjct: 6 GKVTEKVKGGLIVDIE-GVRAFLPASQVD--LRPVEDLDEY-VGKELKFKIIEIDRERNN 61
Query: 1407 I 1407
I
Sbjct: 62 I 62
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 110 bits (277), Expect = 4e-24
Identities = 118/523 (22%), Positives = 211/523 (40%), Gaps = 91/523 (17%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVG--ETMGKYHPHGDVSIYDAL 89
R++P + DGLKP R++LFA + NL N +K A++ G YH HG+ S+ +
Sbjct: 680 RSIPSLVDGLKPGQRKILFACFK-RNLKNE--IKVAQLSGYVSEHSAYH-HGEQSLQQTI 735
Query: 90 VRMAQSF--SLRCTLVDGQGNFGS--IDGDSAAAMRYTECRLNKISNELLIDLDKETIDF 145
V MAQ+F S L+ G FGS G AA RY +L+KI+ + + D D
Sbjct: 736 VGMAQNFVGSNNINLLYPCGQFGSRLQGGKDHAAARYIFTKLSKITRYIFPEED----DP 791
Query: 146 ISNY---DGKEKEPS-VLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNP 201
I +Y DG+ EP +P IP +L+NG+ GI G +T+IP +N ++ID + L+
Sbjct: 792 ILDYLEDDGQSVEPFYYVPI-IPMVLVNGAEGIGTGFSTSIPNYNPLDIIDNLRRRLNG- 849
Query: 202 ECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTG-KGRVIIRAKTHIE---EFNRENRT 257
++ ++P +Y G KG + K + +
Sbjct: 850 ----EEVRPLVP-------------------WYRGFKGTIERNPKGKFISKGIYEKVPDG 886
Query: 258 AIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVL 317
+ I ELP + E + ++K I + RD S + + ++L + +
Sbjct: 887 TVEITELPIGKWTEDYKEFLESETLKEKDV-IVDYRDYSTANTVHFTVKLNDGVLEQWEE 945
Query: 318 NKLYKQTQLQNTFGMNMLALVNGQ---PKLLNLKEILYYFILHRKEVIKRRTIFELRKAR 374
+ K +L++T + L + K + +IL F L R ++ K+R + L K
Sbjct: 946 EGIEKVFKLKSTISTTNMVLFDENGKIKKYSDALDILKEFYLVRLDLYKKRKEYLLGK-- 1003
Query: 375 EYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTI 434
LE L+N FI+ + + +++ + N + K Y
Sbjct: 1004 -----LERELARLSNKVRFIKHVIN--------GELVIT--NAKKKDLVKELKKLGYVRF 1048
Query: 435 SKINNISK---------------LQNNDMYKLSDIQAQE---ILKMPLQRLTNMEQKKII 476
I +++ + A +L MP+ LT K+ +
Sbjct: 1049 KDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLT----KEKV 1104
Query: 477 NKYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKK 519
K ++K + L N+ ++ ++L+ + ++
Sbjct: 1105 EKLNAELEKKEKELEKLKNTT-PKDMWLEDLDKFEEALEEQEE 1146
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 106 bits (267), Expect = 6e-23
Identities = 98/367 (26%), Positives = 156/367 (42%), Gaps = 45/367 (12%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARV------VGETMGKYHPHGDVSI 85
R++P + DGLKP R+VLFA + R +V V E YH HG+ S+
Sbjct: 673 RSIPSMVDGLKPSQRKVLFA------CFKRNLKSEIKVAQLSGYVAE-HSAYH-HGEASL 724
Query: 86 YDALVRMAQSF--SLRCTLVDGQGNFGS--IDGDSAAAMRYTECRLNKISNELLIDLDKE 141
++ MAQ F S L+ G FG+ G AA+ RY RL+ I+ L D
Sbjct: 725 ASTIIGMAQDFVGSNNINLLTPSGQFGTRLQGGKDAASARYIFTRLSPITRALFPKDDDV 784
Query: 142 TIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNP 201
++++ N DG+ EP IP +L+NGS GI G +T IP +N ++I + +L
Sbjct: 785 LLNYL-NEDGQSIEPEWYCPIIPMVLVNGSEGIGTGWSTFIPNYNPRDIIANIRRLLRGE 843
Query: 202 ECSINDLIKIIP-APDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAII 260
E L + P F G I +S+ G YT G + + T I
Sbjct: 844 E-----LEPMHPWYRGF--KGTITEVSTSRSGSYTVTGII-----------EQIGDTTIR 885
Query: 261 IDELPYQV---NKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVL 317
I ELP + + K LE + K+K+ E I + ++ + + + L ++ +
Sbjct: 886 ITELPVRKWTQDYKEFLEALLTGTKKKEPE-IKDFKENHTDTTVHFTVTLSEEKMARALA 944
Query: 318 NKLYKQTQLQNTFGMNMLALVNGQPKLLNLK---EILYYFILHRKEVIKRRTIFELRKAR 374
L K+ +L T + + L + K+ +IL F R ++ +R L
Sbjct: 945 EGLEKKFKLSTTISTSNMHLFDKDGKIKKYDSPEDILEEFFHLRLDLYVKRKEVLLENLE 1004
Query: 375 EYAHILE 381
L+
Sbjct: 1005 YELKKLD 1011
>gnl|CDD|240213 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 77
Score = 78.1 bits (193), Expect = 2e-17
Identities = 32/74 (43%), Positives = 51/74 (68%), Gaps = 2/74 (2%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDG-NIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
K G+KI G ++ + D+G+FI +DG N+ GL H S++S + + + F+ GD++ A +L
Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEIS-DNRVADASKLFRVGDKVRAKVL 59
Query: 1486 SIDVEKERISLGIK 1499
ID EK+RISLG+K
Sbjct: 60 KIDAEKKRISLGLK 73
Score = 68.1 bits (167), Expect = 6e-14
Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 2/73 (2%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDLGGID--GLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
K G + G V+ + DYG FID+ G + GL H ++I+ RV S++ +G + K+LK
Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60
Query: 1313 YDQEKNRVSLGMK 1325
D EK R+SLG+K
Sbjct: 61 IDAEKKRISLGLK 73
Score = 56.2 bits (136), Expect = 1e-09
Identities = 28/73 (38%), Positives = 46/73 (63%), Gaps = 4/73 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIE-KGIEGLVHISEM-DWINKNVTPSKIVQLNDTVEIMILE 1399
G ++ G V + DYG F++I+ + GL H SE+ D N+ SK+ ++ D V +L+
Sbjct: 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISD--NRVADASKLFRVGDKVRAKVLK 60
Query: 1400 INEERRRISLGMK 1412
I+ E++RISLG+K
Sbjct: 61 IDAEKKRISLGLK 73
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a wide
range of RNA associated proteins. It is structurally
similar to cold shock protein which binds nucleic acids.
The S1 domain has an OB-fold structure.
Length = 74
Score = 75.8 bits (187), Expect = 9e-17
Identities = 30/73 (41%), Positives = 50/73 (68%), Gaps = 1/73 (1%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
+EG VKG V +T GAF+DLG G++G + I++I+ RV+ P E+L +G ++ K+LK
Sbjct: 2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLK 61
Query: 1313 YDQEKNRVSLGMK 1325
D+E+ R+ L ++
Sbjct: 62 VDKERGRIILSIR 74
Score = 73.8 bits (182), Expect = 6e-16
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 1426 HKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
++G+ +KG + +T G F+ L ++G I +S++S D E+ K GDE+E +L
Sbjct: 2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISD-DRVEDPDEVLKVGDEVEVKVL 60
Query: 1486 SIDVEKERISLGIK 1499
+D E+ RI L I+
Sbjct: 61 KVDKERGRIILSIR 74
Score = 73.4 bits (181), Expect = 7e-16
Identities = 25/75 (33%), Positives = 48/75 (64%), Gaps = 1/75 (1%)
Query: 1338 RYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMI 1397
+ G + G VT +T GAFV++ G+EG + ISE+ ++ P +++++ D VE+ +
Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISD-DRVEDPDEVLKVGDEVEVKV 59
Query: 1398 LEINEERRRISLGMK 1412
L++++ER RI L ++
Sbjct: 60 LKVDKERGRIILSIR 74
Score = 57.3 bits (139), Expect = 3e-10
Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 1168 ESGEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKD--TTPFEGKTMDFKVIKL 1224
E G+++ GT+ KGG V L NG++ F+P S + V+D G ++ KV+K+
Sbjct: 3 EEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKV 62
Query: 1225 DRKRNNVVLSHR 1236
D++R ++LS R
Sbjct: 63 DKERGRIILSIR 74
Score = 48.8 bits (117), Expect = 3e-07
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKND---NGELEVKIGDFVSVAIESLEN 1142
G+V+ V + + ++ E FIPI E +D + + +K+GD V V + ++
Sbjct: 5 GDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDK 64
Query: 1143 GFGDTILSR 1151
G ILS
Sbjct: 65 ERGRIILSI 73
Score = 43.4 bits (103), Expect = 3e-05
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 1515 KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH----EKKLKIGENIDVLTVLI 1570
+G +V G + + T GA + L N VEG++ ISE + ++ LK+G+ ++V + +
Sbjct: 4 EGDVVKGTVTRV-TKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKV 62
Query: 1571 DHKTRYIQLSFK 1582
D + I LS +
Sbjct: 63 DKERGRIILSIR 74
>gnl|CDD|240190 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription
accessory factor called Tex, which has been characterized
in Bordetella pertussis and Pseudomonas aeruginosa. The
tex gene is essential in Bortella pertusis and is named
for its role in toxin expression. Tex has two functional
domains, an N-terminal domain homologous to the
Escherichia coli maltose repression protein, which is a
poorly defined transcriptional factor, and a C-terminal
S1 RNA-binding domain. Tex is found in prokaryotes,
eukaryotes, and archaea.
Length = 68
Score = 74.6 bits (184), Expect = 3e-16
Identities = 34/69 (49%), Positives = 48/69 (69%), Gaps = 3/69 (4%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNV-TPSKIVQLNDTVEIMILEI 1400
G L G VTN+TD+GAFV+I +GL+HIS+M ++ V PS +V + D VE+ ++ I
Sbjct: 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKM--ADRFVSHPSDVVSVGDIVEVKVISI 58
Query: 1401 NEERRRISL 1409
+EER RISL
Sbjct: 59 DEERGRISL 67
Score = 72.3 bits (178), Expect = 1e-15
Identities = 30/67 (44%), Positives = 50/67 (74%), Gaps = 1/67 (1%)
Query: 1257 GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G ++GVV N+TD+GAF+D+G DGL+HI+ +A R V HPS+++++G + K++ D+
Sbjct: 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE 60
Query: 1316 EKNRVSL 1322
E+ R+SL
Sbjct: 61 ERGRISL 67
Score = 50.7 bits (122), Expect = 5e-08
Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 7/71 (9%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIEAIIL 1485
G ++G++ ++TDFG F+ + DGLIH+S ++ P + + GD +E ++
Sbjct: 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVV----SVGDIVEVKVI 56
Query: 1486 SIDVEKERISL 1496
SID E+ RISL
Sbjct: 57 SIDEERGRISL 67
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 83.8 bits (207), Expect = 7e-16
Identities = 101/369 (27%), Positives = 153/369 (41%), Gaps = 58/369 (15%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARV------VGETMGKYHPHGDVSI 85
R++P + DGLKP R++LF + R FVK A+V V E YH HG+ S+
Sbjct: 698 RSIPSMVDGLKPGQRKILFCS------FKRNFVKEAKVAQLSGYVSE-HSAYH-HGEQSL 749
Query: 86 YDALVRMAQSF--SLRCTLVDGQGNFG--SIDGDSAAAMRYTECRLNKISNELLIDLDKE 141
++ MAQ F S L+ G FG G A+ RY RL+ I+ L D
Sbjct: 750 ASTIIGMAQDFVGSNNINLLLPNGQFGTRLQGGKDHASARYIFTRLSPITRFLFPKDDDI 809
Query: 142 TIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNP 201
+D++ N DG+ EP+ IP +L+NG+ GI G +T IP +N +++ + +L N
Sbjct: 810 LLDYL-NEDGQSIEPTWYMPIIPTVLVNGAEGIGTGWSTFIPNYNPRDIVANIRRLL-NG 867
Query: 202 ECSINDLIKIIPAPDFP-----TAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENR 256
E P P I S YT G EE +
Sbjct: 868 ES---------MEPMHPWYRGFKGTIEKTASKEGGCTYTITGL--------YEEV---DE 907
Query: 257 TAIIIDELP---YQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIEL---KRN 310
T + I ELP + + K LE + + K I +++ +D + + + L
Sbjct: 908 TTLRITELPIRRWTDDYKEFLESLKTDNNKNKDPFIKDVKAYNDDTTVHFEVILSEENML 967
Query: 311 EIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFI-------LHRKEVIK 363
+ L K +K T +T M++ K ++IL F RKEV+
Sbjct: 968 AAKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQILEEFFHLRLEYYEKRKEVLL 1027
Query: 364 RRTIFELRK 372
+ FEL K
Sbjct: 1028 KNLEFELLK 1036
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 73.4 bits (181), Expect = 7e-16
Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
+ G+ ++G + IT G F+ L ++GLI +S+LS ++ K GDE++ +LS
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSD-KRVKDPEEVLKVGDEVKVKVLS 59
Query: 1487 IDVEKERISLGIK 1499
+D EK RI L +K
Sbjct: 60 VDEEKGRIILSLK 72
Score = 73.0 bits (180), Expect = 9e-16
Identities = 31/72 (43%), Positives = 50/72 (69%), Gaps = 1/72 (1%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKY 1313
+ G V+G V IT GAF+DLG G++GL+ I++++ +RVK P E+L +G ++ K+L
Sbjct: 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 1314 DQEKNRVSLGMK 1325
D+EK R+ L +K
Sbjct: 61 DEEKGRIILSLK 72
Score = 72.3 bits (178), Expect = 2e-15
Identities = 26/71 (36%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
G + G VT +T GAFV++ G+EGL+ ISE+ + P +++++ D V++ +L ++
Sbjct: 3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSD-KRVKDPEEVLKVGDEVKVKVLSVD 61
Query: 1402 EERRRISLGMK 1412
EE+ RI L +K
Sbjct: 62 EEKGRIILSLK 72
Score = 46.4 bits (111), Expect = 2e-06
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 1170 GEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMDFKVIKLDR 1226
G+++ GT+ GG V L NG++ +P S + + VKD G + KV+ +D
Sbjct: 3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62
Query: 1227 KRNNVVLSHR 1236
++ ++LS +
Sbjct: 63 EKGRIILSLK 72
Score = 46.1 bits (110), Expect = 3e-06
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 5/72 (6%)
Query: 1515 KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH----EKKLKIGENIDVLTVLI 1570
G +V G + I T GA + L N VEG + ISE +K E+ LK+G+ + V + +
Sbjct: 2 VGDVVEGTVTEI-TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 1571 DHKTRYIQLSFK 1582
D + I LS K
Sbjct: 61 DEEKGRIILSLK 72
Score = 35.3 bits (82), Expect = 0.019
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNG---ELEVKIGDFVSVAIESLEN 1142
G+V+ V + ++ E IPI E + E +K+GD V V + S++
Sbjct: 3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDE 62
Query: 1143 GFGDTILSR 1151
G ILS
Sbjct: 63 EKGRIILSL 71
>gnl|CDD|238094 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding
domain. Found in a wide variety of RNA-associated
proteins. Originally identified in S1 ribosomal protein.
This superfamily also contains the Cold Shock Domain
(CSD), which is a homolog of the S1 domain. Both domains
are members of the Oligonucleotide/oligosaccharide
Binding (OB) fold.
Length = 65
Score = 72.8 bits (179), Expect = 9e-16
Identities = 27/65 (41%), Positives = 46/65 (70%), Gaps = 1/65 (1%)
Query: 1260 VKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKN 1318
V G V +IT +G F++L G++GL+HI++++ + VK PSE+ +G ++ K+L+ D EK
Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60
Query: 1319 RVSLG 1323
R+SL
Sbjct: 61 RISLS 65
Score = 71.3 bits (175), Expect = 3e-15
Identities = 30/64 (46%), Positives = 45/64 (70%), Gaps = 1/64 (1%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRR 1406
GKV ++T +G FVE+E G+EGLVHISE+ PS++ ++ D VE+ +LE++ E+ R
Sbjct: 3 GKVVSITKFGVFVELEDGVEGLVHISELSD-KFVKDPSEVFKVGDEVEVKVLEVDPEKGR 61
Query: 1407 ISLG 1410
ISL
Sbjct: 62 ISLS 65
Score = 67.0 bits (164), Expect = 1e-13
Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 1/66 (1%)
Query: 1432 IKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEK 1491
+ G + SIT FG+F+ L+ ++GL+H+S+LS ++ FK GDE+E +L +D EK
Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-KDPSEVFKVGDEVEVKVLEVDPEK 59
Query: 1492 ERISLG 1497
RISL
Sbjct: 60 GRISLS 65
Score = 37.0 bits (86), Expect = 0.004
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 1519 VNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH----EKKLKIGENIDVLTVLIDHKT 1574
V G + SI T G ++L + VEG + ISE +K + K+G+ ++V + +D +
Sbjct: 1 VTGKVVSI-TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEK 59
Query: 1575 RYIQLS 1580
I LS
Sbjct: 60 GRISLS 65
>gnl|CDD|240192 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal
protein S1 (RPS1) domain. RPS1 is a component of the
small ribosomal subunit thought to be involved in the
recognition and binding of mRNA's during translation
initiation. The bacterial RPS1 domain architecture
consists of 4-6 tandem S1 domains. In some bacteria, the
tandem S1 array is located C-terminal to a
4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP
reductase) domain. While RPS1 is found primarily in
bacteria, proteins with tandem RPS1-like domains have
been identified in plants and humans, however these lack
the N-terminal HMBPP reductase domain. This CD includes
S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1
(ec1 and hs1, respectively). Autoantibodies to
double-stranded DNA from patients with systemic lupus
erythematosus cross-react with the human RPS1 homolog.
Length = 70
Score = 72.6 bits (179), Expect = 1e-15
Identities = 27/70 (38%), Positives = 44/70 (62%), Gaps = 3/70 (4%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKND---NGELEVKIGDFVSVAIESLEN 1142
G+++ V+ +D + V+++ KSE IPI EF +D NGE EVK+GD V V + +E+
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60
Query: 1143 GFGDTILSRD 1152
G+ +LS+
Sbjct: 61 EEGNVVLSKR 70
Score = 43.3 bits (103), Expect = 3e-05
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G+ +KG + S+ D + + + +G+I +S+ S DP E K GDE+E +L ++
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFS-DDPIENGEDEVKVGDEVEVYVLRVE 59
Query: 1489 VEKERISLGIK 1499
E+ + L +
Sbjct: 60 DEEGNVVLSKR 70
Score = 36.4 bits (85), Expect = 0.008
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
G + G V ++ D V+I EG++ ISE + V++ D VE+ +L +
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFS-DDPIENGEDEVKVGDEVEVYVLRVE 59
Query: 1402 EERRRISL 1409
+E + L
Sbjct: 60 DEEGNVVL 67
Score = 35.6 bits (83), Expect = 0.013
Identities = 15/67 (22%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 1257 GCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G VKG V ++ D +D+G +G++ I++ + +++ + + +G ++ +L+ +
Sbjct: 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVED 60
Query: 1316 EKNRVSL 1322
E+ V L
Sbjct: 61 EEGNVVL 67
Score = 34.8 bits (81), Expect = 0.024
Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISE----EDNKHEKKLKIGENIDVLTVLID 1571
G +V G + S+D + ++ + + EG + ISE E ++K+G+ ++V + ++
Sbjct: 1 GDIVKGTVVSVD-DDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVE 59
Query: 1572 HKTRYIQLSFK 1582
+ + LS +
Sbjct: 60 DEEGNVVLSKR 70
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 78.2 bits (194), Expect = 2e-14
Identities = 27/79 (34%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 1250 LIETLKEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWRRVKHPSEILTIGQDIST 1308
+ + G +G V I D+GAF++ L G DGL+HI++IA RV+ ++L G ++
Sbjct: 615 ITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKV 674
Query: 1309 KILKYDQEKNRVSLGMKQL 1327
K+L+ D ++ R+ L K +
Sbjct: 675 KVLEID-KRGRIRLSRKAV 692
Score = 77.8 bits (193), Expect = 3e-14
Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW--INKNVTPSKIVQLNDTVEIMILE 1399
G GKV + D+GAFVEI G +GLVHISE+ + K +++ D V++ +LE
Sbjct: 622 GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEK---VEDVLKEGDEVKVKVLE 678
Query: 1400 INEERRRISLGMK 1412
I+ +R RI L K
Sbjct: 679 ID-KRGRIRLSRK 690
Score = 55.1 bits (134), Expect = 3e-07
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKKGDEIEA 1482
+ GE +G + I DFG F+ + DGL+H+S+++ E + K+GDE++
Sbjct: 620 EVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIAD-----ERVEKVEDVLKEGDEVKV 674
Query: 1483 IILSIDVEKERISLGIKQLE 1502
+L ID ++ RI L K +
Sbjct: 675 KVLEID-KRGRIRLSRKAVL 693
Score = 37.7 bits (89), Expect = 0.053
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
G + G + I + GA +++ +G + ISE ++ +K LK G+ + V + ID
Sbjct: 622 GEIYEGKVVRI-VDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680
Query: 1572 HKTRYIQLSFK 1582
+ R I+LS K
Sbjct: 681 KRGR-IRLSRK 690
>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription].
Length = 780
Score = 77.3 bits (191), Expect = 4e-14
Identities = 28/77 (36%), Positives = 52/77 (67%), Gaps = 1/77 (1%)
Query: 1251 IETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTK 1309
I LK G ++G V+N+ D+GAF+D+G DGL+HI+ ++ + VK P+E++ +G + K
Sbjct: 653 ITDLKPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVK 712
Query: 1310 ILKYDQEKNRVSLGMKQ 1326
+++ D + R++L M+
Sbjct: 713 VIEVDTARKRIALSMRL 729
Score = 65.4 bits (160), Expect = 2e-10
Identities = 29/73 (39%), Positives = 50/73 (68%), Gaps = 3/73 (4%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNV-TPSKIVQLNDTVEIMILEI 1400
G L G V N+ D+GAFV+I +GLVHIS++ +K V P+++V++ D V++ ++E+
Sbjct: 659 GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS--DKFVKDPNEVVKVGDIVKVKVIEV 716
Query: 1401 NEERRRISLGMKQ 1413
+ R+RI+L M+
Sbjct: 717 DTARKRIALSMRL 729
Score = 49.6 bits (119), Expect = 2e-05
Identities = 21/74 (28%), Positives = 45/74 (60%), Gaps = 9/74 (12%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKKGDEIEA 1482
K G ++G ++++ DFG F+ + + DGL+H+S LS ++ +++ K GD ++
Sbjct: 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLS-----DKFVKDPNEVVKVGDIVKV 711
Query: 1483 IILSIDVEKERISL 1496
++ +D ++RI+L
Sbjct: 712 KVIEVDTARKRIAL 725
Score = 30.7 bits (70), Expect = 9.0
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 1508 NYVNIND--KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEE-----DNKHEKKLKIG 1560
+I D G ++ G ++++ + GA + + +G + IS+ + +E +K+G
Sbjct: 649 GVESITDLKPGMILEGTVRNV-VDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEV-VKVG 706
Query: 1561 ENIDVLTVLIDHKTRYIQLSFKKKEV 1586
+ + V + +D + I LS + E
Sbjct: 707 DIVKVKVIEVDTARKRIALSMRLDEE 732
>gnl|CDD|240197 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1
(RPS1) domain. RPS1 is a component of the small ribosomal
subunit thought to be involved in the recognition and
binding of mRNA's during translation initiation. The
bacterial RPS1 domain architecture consists of 4-6 tandem
S1 domains. In some bacteria, the tandem S1 array is
located C-terminal to a 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase (HMBPP reductase) domain. While
RPS1 is found primarily in bacteria, proteins with tandem
RPS1-like domains have been identified in plants and
humans, however these lack the N-terminal HMBPP reductase
domain. This CD includes S1 repeat 4 (hs4) of the H.
sapiens RPS1 homolog. Autoantibodies to double-stranded
DNA from patients with systemic lupus erythematosus
cross-react with the human RPS1 homolog.
Length = 69
Score = 64.6 bits (158), Expect = 8e-13
Identities = 29/70 (41%), Positives = 43/70 (61%), Gaps = 2/70 (2%)
Query: 1257 GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G V+G V + +GAF++LG GI GL+HI+ IA +RVK ++L G + K+L D
Sbjct: 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60
Query: 1316 EKNRVSLGMK 1325
R+SL +K
Sbjct: 61 RG-RISLSIK 69
Score = 64.2 bits (157), Expect = 1e-12
Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEI 1400
G+ + G VT L +GAFVE+ GI GLVHIS++ +K V +++ D V++ +L I
Sbjct: 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIA--HKRVKDVKDVLKEGDKVKVKVLSI 58
Query: 1401 NEERRRISLGMK 1412
+ R RISL +K
Sbjct: 59 -DARGRISLSIK 69
Score = 50.4 bits (121), Expect = 8e-08
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 8/74 (10%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSW---TDPGEEIIRNFKKGDEIEAIIL 1485
G ++G + + FG F+ L G I GL+H+S ++ D + + K+GD+++ +L
Sbjct: 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVL----KEGDKVKVKVL 56
Query: 1486 SIDVEKERISLGIK 1499
SID + RISL IK
Sbjct: 57 SID-ARGRISLSIK 69
Score = 36.5 bits (85), Expect = 0.007
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
GS+V G + + GA ++L + G + IS+ +K K LK G+ + V + ID
Sbjct: 1 GSVVEGTVTRL-KPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID 59
Query: 1572 HKTRYIQLSFK 1582
+ R I LS K
Sbjct: 60 ARGR-ISLSIK 69
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated.
Length = 123
Score = 63.9 bits (156), Expect = 6e-12
Identities = 28/83 (33%), Positives = 51/83 (61%), Gaps = 3/83 (3%)
Query: 1339 YPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM-DWINKNVTPSKIVQLNDTVEIMI 1397
Y G+ + GKVT + YGAFV +++ +GLVHISE+ K++ + + D V++ +
Sbjct: 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDI--HDFLSVGDEVKVKV 62
Query: 1398 LEINEERRRISLGMKQCKDNPWE 1420
L ++EE+ +ISL ++ ++ P
Sbjct: 63 LSVDEEKGKISLSIRATEEAPEA 85
Score = 62.8 bits (153), Expect = 2e-11
Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 1252 ETLKEGCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKI 1310
+ G V G V I YGAF+ L GL+HI++I VK + L++G ++ K+
Sbjct: 3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKV 62
Query: 1311 LKYDQEKNRVSLGMK 1325
L D+EK ++SL ++
Sbjct: 63 LSVDEEKGKISLSIR 77
Score = 53.1 bits (128), Expect = 3e-08
Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 17/87 (19%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKK--------GD 1478
+ G + G + I +G F+ LD GL+H+S EI F K GD
Sbjct: 6 EVGSVVTGKVTGIQPYGAFVALDEETQGLVHIS---------EITHGFVKDIHDFLSVGD 56
Query: 1479 EIEAIILSIDVEKERISLGIKQLEGDP 1505
E++ +LS+D EK +ISL I+ E P
Sbjct: 57 EVKVKVLSVDEEKGKISLSIRATEEAP 83
Score = 31.9 bits (73), Expect = 0.93
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
GS+V G + I GA + L E +G + ISE + K L +G+ + V + +D
Sbjct: 8 GSVVTGKVTGIQP-YGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVD 66
Query: 1572 HKTRYIQLSFKKKEVIKKKK 1591
+ I LS + E + K
Sbjct: 67 EEKGKISLSIRATEEAPEAK 86
>gnl|CDD|240189 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1
domain of human ATP-dependent RNA helicase DHX8, a DEAH
(Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA
helicases are thought to play key roles in pre-mRNA
splicing and DHX8 facilitates nuclear export of spliced
mRNA by releasing the RNA from the spliceosome. DHX8 is
also known as HRH1 (human RNA helicase 1) in Homo sapiens
and PRP22 in Saccharomyces cerevisiae.
Length = 79
Score = 61.9 bits (151), Expect = 9e-12
Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 5/69 (7%)
Query: 1347 GKVTNLTDYGAFVEIE---KGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEE 1403
GKVT++ D+G FV++E EGLVHIS++ + + PS +V+ V++ ++ I +
Sbjct: 6 GKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISI--Q 63
Query: 1404 RRRISLGMK 1412
+ISL MK
Sbjct: 64 NGKISLSMK 72
Score = 58.8 bits (143), Expect = 1e-10
Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 9/75 (12%)
Query: 1261 KGVVKNITDYGAFIDL----GGIDGLLHITDIAW-RRVKHPSEILTIGQDISTKILKYDQ 1315
KG V +I D+G F+ L G +GL+HI+ +++ RV +PS+++ GQ + K++
Sbjct: 5 KGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISI-- 62
Query: 1316 EKNRVSLGMKQLGID 1330
+ ++SL MK +D
Sbjct: 63 QNGKISLSMK--DVD 75
Score = 43.0 bits (102), Expect = 4e-05
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 1433 KGIIKSITDFGIFI---GLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDV 1489
KG + SI DFG F+ GL G +GL+H+S LS+ K+G +++ ++SI
Sbjct: 5 KGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISI-- 62
Query: 1490 EKERISLGIK 1499
+ +ISL +K
Sbjct: 63 QNGKISLSMK 72
>gnl|CDD|240196 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1
(RPS1) domain. RPS1 is a component of the small ribosomal
subunit thought to be involved in the recognition and
binding of mRNA's during translation initiation. The
bacterial RPS1 domain architecture consists of 4-6 tandem
S1 domains. In some bacteria, the tandem S1 array is
located C-terminal to a 4-hydroxy-3-methylbut-2-enyl
diphosphate reductase (HMBPP reductase) domain. While
RPS1 is found primarily in bacteria, proteins with tandem
RPS1-like domains have been identified in plants and
humans, however these lack the N-terminal HMBPP reductase
domain. This CD includes S1 repeat 6 (ec6) of the
Escherichia coli RPS1. Autoantibodies to double-stranded
DNA from patients with systemic lupus erythematosus
cross-react with the human RPS1 homolog.
Length = 73
Score = 61.5 bits (150), Expect = 1e-11
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 5/74 (6%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLR---ISEEDNKHE-KKLKIGENIDVLTVLID 1571
GS+V G + +D KGA ++L + VEG+LR +S + + ++ K+G+ ++ +D
Sbjct: 1 GSIVTGKVTEVD-AKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVD 59
Query: 1572 HKTRYIQLSFKKKE 1585
K R I LS K KE
Sbjct: 60 RKNRKISLSIKAKE 73
Score = 52.7 bits (127), Expect = 2e-08
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 1257 GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G V G V + GA + LG G++G L +++ RV+ +E +G ++ KI D+
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60
Query: 1316 EKNRVSLGMKQL 1327
+ ++SL +K
Sbjct: 61 KNRKISLSIKAK 72
Score = 51.9 bits (125), Expect = 3e-08
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G + G + + G + L ++G + ++LS D E+ FK GDE+EA I ++D
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELS-RDRVEDATERFKVGDEVEAKITNVD 59
Query: 1489 VEKERISLGIKQLE 1502
+ +ISL IK E
Sbjct: 60 RKNRKISLSIKAKE 73
Score = 34.6 bits (80), Expect = 0.040
Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 1170 GEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMDFKVIKLDR 1226
G I+TG + G TV L +G++ FL + + V+D T G ++ K+ +DR
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDR 60
Query: 1227 KRNNVVLSHRAV 1238
K + LS +A
Sbjct: 61 KNRKISLSIKAK 72
Score = 31.9 bits (73), Expect = 0.28
Identities = 21/72 (29%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
G+ + GKVT + GA V++ G+EG + +E+ ++ ++ ++ D VE I ++
Sbjct: 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELS-RDRVEDATERFKVGDEVEAKITNVD 59
Query: 1402 EERRRISLGMKQ 1413
+ R+ISL +K
Sbjct: 60 RKNRKISLSIKA 71
>gnl|CDD|239918 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase),
), S1-like RNA-binding domain. PNPase is a
polyribonucleotide nucleotidyl transferase that degrades
mRNA. It is a trimeric multidomain protein. The
C-terminus contains the S1 domain which binds ssRNA. This
family is classified based on the S1 domain. PNPase
nonspecifically removes the 3' nucleotides from mRNA, but
is stalled by double-stranded RNA structures such as a
stem-loop. Evidence shows that a minimum of 7-10 unpaired
nucleotides at the 3' end, is required for PNPase
degradation. It is suggested that PNPase also
dephosphorylates the RNA 5' end. This additional activity
may regulate the 5'-dependent activity of RNaseE in vivo.
Length = 68
Score = 60.2 bits (147), Expect = 2e-11
Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 6/70 (8%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMD--WINKNVTPSKIVQLNDTVEIMILE 1399
G GKV + D+GAFVEI G +GLVHISE+ + K ++++ D V++ ++E
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEK---VEDVLKVGDEVKVKVIE 57
Query: 1400 INEERRRISL 1409
++ +R RISL
Sbjct: 58 VD-DRGRISL 66
Score = 59.5 bits (145), Expect = 4e-11
Identities = 24/67 (35%), Positives = 45/67 (67%), Gaps = 2/67 (2%)
Query: 1257 GCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G +G V I D+GAF++ L G DGL+HI++++ RV+ ++L +G ++ K+++ D
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD- 59
Query: 1316 EKNRVSL 1322
++ R+SL
Sbjct: 60 DRGRISL 66
Score = 41.4 bits (98), Expect = 1e-04
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 10/72 (13%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKKGDEIEAII 1484
G+ +G + I DFG F+ + DGL+H+S+LS +E + K GDE++ +
Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELS-----DERVEKVEDVLKVGDEVKVKV 55
Query: 1485 LSIDVEKERISL 1496
+ +D ++ RISL
Sbjct: 56 IEVD-DRGRISL 66
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model TIGR02696
for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 66.4 bits (163), Expect = 1e-10
Identities = 30/85 (35%), Positives = 50/85 (58%), Gaps = 6/85 (7%)
Query: 1243 MGEERQKLIETL----KEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWRRVKHPS 1297
E K+IE + + G +G V I D+GAF++ L G DGL+HI++IA RV+
Sbjct: 601 AAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVE 660
Query: 1298 EILTIGQDISTKILKYDQEKNRVSL 1322
++L G ++ K+L+ D ++ R+ L
Sbjct: 661 DVLKEGDEVKVKVLEID-KQGRIKL 684
Score = 65.2 bits (160), Expect = 2e-10
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 6/70 (8%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW--INKNVTPSKIVQLNDTVEIMILE 1399
G GKV + D+GAFVEI G +GLVHISE+ + K +++ D V++ +LE
Sbjct: 619 GKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEK---VEDVLKEGDEVKVKVLE 675
Query: 1400 INEERRRISL 1409
I+ ++ RI L
Sbjct: 676 ID-KQGRIKL 684
Score = 46.3 bits (111), Expect = 1e-04
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 10/72 (13%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKKGDEIEAII 1484
G+ +G + I DFG F+ + DGL+H+S+++ E + K+GDE++ +
Sbjct: 619 GKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIAN-----ERVEKVEDVLKEGDEVKVKV 673
Query: 1485 LSIDVEKERISL 1496
L ID ++ RI L
Sbjct: 674 LEID-KQGRIKL 684
Score = 32.5 bits (75), Expect = 2.0
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH----EKKLKIGENIDVLTVLID 1571
G + G + I + GA +++ +G + ISE N+ E LK G+ + V + ID
Sbjct: 619 GKIYEGKVVRI-MDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEID 677
Query: 1572 HKTRYIQL 1579
+ R I+L
Sbjct: 678 KQGR-IKL 684
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo
sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1
repeat 7 (sc7)-like domains. Rrp5 is a trans-acting
factor important for biogenesis of both the 40S and 60S
eukaryotic ribosomal subunits. Rrp5 has two distinct
regions, an N-terminal region containing tandemly
repeated S1 RNA-binding domains (12 S1 repeats in S.
cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and
a C-terminal region containing tetratricopeptide repeat
(TPR) motifs thought to be involved in protein-protein
interactions. Mutational studies have shown that each
region represents a specific functional domain. Deletions
within the S1-containing region inhibit pre-rRNA
processing at either site A3 or A2, whereas deletions
within the TPR region confer an inability to support
cleavage of A0-A2. This CD includes H. sapiens S1 repeat
8 and S. cerevisiae S1 repeat 7. Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 83
Score = 59.1 bits (144), Expect = 1e-10
Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 1249 KLIETLKEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWRRVKHPSEILTIGQDIS 1307
LK G V G V+NIT YG F++ LGG+ GL + I+ V PS GQ ++
Sbjct: 7 TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVT 66
Query: 1308 TKILKYDQEKNRVSLGM 1324
K+ D+EK R L +
Sbjct: 67 AKVTSVDEEKQRFLLSL 83
Score = 47.2 bits (113), Expect = 2e-06
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 10/80 (12%)
Query: 1421 NFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKK 1476
NFS + K G + G +++IT +G+F+ G + GL S +S +E + + FKK
Sbjct: 8 NFSDL-KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYIS-----DEFVTDPSFGFKK 61
Query: 1477 GDEIEAIILSIDVEKERISL 1496
G + A + S+D EK+R L
Sbjct: 62 GQSVTAKVTSVDEEKQRFLL 81
Score = 47.2 bits (113), Expect = 2e-06
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEI 1400
G + G V N+T YG FVE G+ GL S + ++ VT PS + +V + +
Sbjct: 15 GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYI--SDEFVTDPSFGFKKGQSVTAKVTSV 72
Query: 1401 NEERRRISLGM 1411
+EE++R L +
Sbjct: 73 DEEKQRFLLSL 83
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 65.7 bits (161), Expect = 2e-10
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW--INKNVTPSKIVQLNDTVEIMILE 1399
G G V + D+GAFVE+ G +GLVHIS++ + K +++ D V++ ++E
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEK---VEDVLKEGDEVKVKVIE 676
Query: 1400 INEERRRISLGMK 1412
I+ ++ RI L +K
Sbjct: 677 ID-KQGRIRLSIK 688
Score = 64.5 bits (158), Expect = 4e-10
Identities = 27/82 (32%), Positives = 49/82 (59%), Gaps = 6/82 (7%)
Query: 1249 KLIETL----KEGCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIG 1303
+ IE + + G +G V I D+GAF++L G DGL+HI+ +A RV+ ++L G
Sbjct: 608 ERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEG 667
Query: 1304 QDISTKILKYDQEKNRVSLGMK 1325
++ K+++ D ++ R+ L +K
Sbjct: 668 DEVKVKVIEID-KQGRIRLSIK 688
Score = 51.8 bits (125), Expect = 3e-06
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 10/79 (12%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNF----KKGDEIEAII 1484
GE +G + I DFG F+ L DGL+H+S L+ E + K+GDE++ +
Sbjct: 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAK-----ERVEKVEDVLKEGDEVKVKV 674
Query: 1485 LSIDVEKERISLGIKQLEG 1503
+ ID ++ RI L IK +
Sbjct: 675 IEID-KQGRIRLSIKAVLE 692
Score = 32.2 bits (74), Expect = 2.6
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEED----NKHEKKLKIGENIDVLTVLID 1571
G + G + I + GA ++L +G + IS+ K E LK G+ + V + ID
Sbjct: 620 GEVYEGTVVRI-VDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID 678
Query: 1572 HKTRYIQLSFK 1582
+ R I+LS K
Sbjct: 679 KQGR-IRLSIK 688
>gnl|CDD|224023 COG1098, VacB, Predicted RNA binding protein (contains ribosomal
protein S1 domain) [Translation, ribosomal structure and
biogenesis].
Length = 129
Score = 59.6 bits (145), Expect = 2e-10
Identities = 31/78 (39%), Positives = 52/78 (66%), Gaps = 4/78 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISE-MDWINKNVTPSKIVQLNDTVEIMILEI 1400
G++L GK+T +T YGAFVE+E G GLVHISE D K++ +++ V++ +L+I
Sbjct: 6 GSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDI--HDHLKVGQEVKVKVLDI 63
Query: 1401 NEERRRISLGMKQCKDNP 1418
+E +ISL +++ ++ P
Sbjct: 64 -DENGKISLSIRKLEEEP 80
Score = 58.4 bits (142), Expect = 6e-10
Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 2/76 (2%)
Query: 1253 TLKEGCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
++K G +KG + IT YGAF++L GG GL+HI++IA VK + L +GQ++ K+L
Sbjct: 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVL 61
Query: 1312 KYDQEKNRVSLGMKQL 1327
D E ++SL +++L
Sbjct: 62 DID-ENGKISLSIRKL 76
Score = 54.6 bits (132), Expect = 1e-08
Identities = 31/79 (39%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
K G K+KG I IT +G F+ L+G GL+H+S+++ ++I + K G E++ +L
Sbjct: 4 KVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA-DGFVKDIHDHLKVGQEVKVKVLD 62
Query: 1487 IDVEKERISLGIKQLEGDP 1505
ID E +ISL I++LE +P
Sbjct: 63 ID-ENGKISLSIRKLEEEP 80
Score = 29.6 bits (67), Expect = 5.7
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISE-----EDNKHEKKLKIGENIDVLTVLI 1570
GS + G I I T GA ++L G + ISE + H+ LK+G+ + V + I
Sbjct: 6 GSKLKGKITGI-TPYGAFVELEGGKTGLVHISEIADGFVKDIHD-HLKVGQEVKVKVLDI 63
Query: 1571 DHKTRYIQLSFKKKEVIKKKK 1591
D + I LS +K E +K+
Sbjct: 64 DENGK-ISLSIRKLEEEPEKQ 83
>gnl|CDD|236305 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 58.5 bits (142), Expect = 6e-10
Identities = 33/78 (42%), Positives = 54/78 (69%), Gaps = 4/78 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM-DWINKNVTPSKIVQLNDTVEIMILEI 1400
G++L GKVT +T++GAFVE+ +G GLVHISE+ D K++ + +++ D VE+ +L +
Sbjct: 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDI--NDHLKVGDEVEVKVLNV 63
Query: 1401 NEERRRISLGMKQCKDNP 1418
E+ +I L +K+ KD P
Sbjct: 64 -EDDGKIGLSIKKAKDRP 80
Score = 48.1 bits (115), Expect = 3e-06
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 15/83 (18%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G ++G V IT++GAF++L G GL+HI+++A VK ++ L +G ++ K+L +
Sbjct: 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED 65
Query: 1316 EKNRVSLGMKQLGIDPWIGLSFR 1338
D IGLS +
Sbjct: 66 --------------DGKIGLSIK 74
Score = 42.7 bits (101), Expect = 2e-04
Identities = 24/72 (33%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G K++G + IT+FG F+ L GL+H+S+++ + ++I + K GDE+E +L+++
Sbjct: 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVA-DNYVKDINDHLKVGDEVEVKVLNVE 64
Query: 1489 VEKERISLGIKQ 1500
+ +I L IK+
Sbjct: 65 -DDGKIGLSIKK 75
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 57.7 bits (139), Expect = 6e-10
Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 2/106 (1%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
+I I GP SGK T+A+ +A KLG + L R L+ +++ D +++L +L +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEI 60
Query: 921 LNYNFLGKEVYLNGV-NVTTLIRNEKVSNNASKIAKFKNIRKELFK 965
L+ +E ++GV T +R E+ R L K
Sbjct: 61 LD-ELAKQEWVIDGVRESTLELRLEEADLVVFLDLPLPACRFRLLK 105
>gnl|CDD|235614 PRK05807, PRK05807, hypothetical protein; Provisional.
Length = 136
Score = 55.9 bits (135), Expect = 5e-09
Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 1253 TLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
TLK G ++G V NIT++GAF+++ G GL+HI+++A VK E L + K++
Sbjct: 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVIS 61
Query: 1313 YDQEKNRVSLGMKQ 1326
D + ++SL +KQ
Sbjct: 62 ID-DNGKISLSIKQ 74
Score = 48.6 bits (116), Expect = 2e-06
Identities = 30/73 (41%), Positives = 49/73 (67%), Gaps = 5/73 (6%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM-DWINKNVTPSKIVQLNDTVEIMILEI 1400
G+ L G V N+T++GAFVE+E G GLVHISE+ D K++ + ++ D V++ ++ I
Sbjct: 6 GSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDI--REHLKEQDKVKVKVISI 62
Query: 1401 NEERRRISLGMKQ 1413
++ +ISL +KQ
Sbjct: 63 -DDNGKISLSIKQ 74
Score = 47.0 bits (112), Expect = 6e-06
Identities = 27/75 (36%), Positives = 49/75 (65%), Gaps = 5/75 (6%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNF-KKGDEIEAIIL 1485
K G ++G + +IT+FG F+ ++G GL+H+S+++ D + IR K+ D+++ ++
Sbjct: 4 KAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVA--DTYVKDIREHLKEQDKVKVKVI 60
Query: 1486 SIDVEKERISLGIKQ 1500
SID + +ISL IKQ
Sbjct: 61 SID-DNGKISLSIKQ 74
>gnl|CDD|217832 pfam03989, DNA_gyraseA_C, DNA gyrase C-terminal domain,
beta-propeller. This repeat is found as 6 tandem copies
at the C-termini of GyrA and ParC DNA gyrases. It is
predicted to form 4 beta strands and to probably form a
beta-propeller structure. This region has been shown to
bind DNA non-specifically and may stabilise the
DNA-topoisomerase complex.
Length = 48
Score = 52.1 bits (126), Expect = 1e-08
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 702 DIMLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQKVIALLVSN 748
D++L + G R + GR +GV G++L++ KV+++LV N
Sbjct: 2 DLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIKLKEGDKVVSVLVVN 48
Score = 51.3 bits (124), Expect = 2e-08
Identities = 16/48 (33%), Positives = 30/48 (62%)
Query: 543 DMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIAN 590
D ++ +++ GY+K P+SE+ Q RGG+G K + K+ D + + + N
Sbjct: 1 DDLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIKLKEGDKVVSVLVVN 48
Score = 47.9 bits (115), Expect = 3e-07
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 752 QSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVN 800
+L T GY KRT + E+ + RG KG+ IK + KVV+ +VN
Sbjct: 1 DDLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIKLKE-GDKVVSVLVVN 48
Score = 44.8 bits (107), Expect = 5e-06
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 803 HEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGV 846
+++LIT+ G + RT +SE + GR +GV I ++ K+ V
Sbjct: 1 DDLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIKLKEGDKVVSV 44
Score = 41.7 bits (99), Expect = 5e-05
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 593 DYILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLS 643
D +L ++ G + + + P+ R +G I LK +K+ +L ++
Sbjct: 1 DDLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIK---LKEGDKVVSVLVVN 48
Score = 36.7 bits (86), Expect = 0.004
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 653 NYVFMSTSLGIVKKTLLSNFSNPR--KSGIIAVNLSNEDFLIGAALTD 698
+ + + TS G VK+T LS F G+ + L D ++ + +
Sbjct: 1 DDLLLITSKGYVKRTPLSEFPEQGRGGKGVKGIKLKEGDKVVSVLVVN 48
>gnl|CDD|240202 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat
5 (sc5). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 69
Score = 52.6 bits (127), Expect = 1e-08
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 7/71 (9%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLI---HLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
G+ +KG I+ + GIF+ L +I GL+ HL+D+ P + FK G +++ +L
Sbjct: 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHP----EKKFKPGLKVKCRVL 56
Query: 1486 SIDVEKERISL 1496
S++ E++R+ L
Sbjct: 57 SVEPERKRLVL 67
Score = 42.6 bits (101), Expect = 5e-05
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGL---LHITDIAWRRVKHPSEILTIGQDISTKILK 1312
G VKG ++ + G F+ L I GL +H+ D+ R+KHP + G + ++L
Sbjct: 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV---RLKHPEKKFKPGLKVKCRVLS 57
Query: 1313 YDQEKNRVSL 1322
+ E+ R+ L
Sbjct: 58 VEPERKRLVL 67
Score = 36.1 bits (84), Expect = 0.009
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLV---HISEMDWINKNVTPSKIVQLNDTVEIMILEINEE 1403
G + L G FV++ I+GLV H++ D K+ P K + V+ +L + E
Sbjct: 6 GTIRKLRPSGIFVKLSDHIKGLVPPMHLA--DVRLKH--PEKKFKPGLKVKCRVLSVEPE 61
Query: 1404 RRRISL 1409
R+R+ L
Sbjct: 62 RKRLVL 67
>gnl|CDD|239899 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation
Initiation Factor 2, S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. Eukaryotic and archaeal
Initiation Factor 2 (e- and aIF2, respectively) are
heterotrimeric proteins with three subunits (alpha, beta,
and gamma). IF2 plays a crucial role in the process of
translation initiation. The IF2 gamma subunit contains a
GTP-binding site. The IF2 beta and gamma subunits
together are thought to be responsible for binding
methionyl-initiator tRNA. The ternary complex consisting
of IF2, GTP, and the methionyl-initiator tRNA binds to
the small subunit of the ribosome, as part of a
pre-initiation complex that scans the mRNA to find the
AUG start codon. The IF2-bound GTP is hydrolyzed to GDP
when the methionyl-initiator tRNA binds the AUG start
codon, at which time the IF2 is released with its bound
GDP. The large ribosomal subunit then joins with the
small subunit to complete the initiation complex, which
is competent to begin translation. The IF2a subunit is a
major site of control of the translation initiation
process, via phosphorylation of a specific serine
residue. This alpha subunit is well conserved in
eukaryotes and archaea but is not present in bacteria.
IF2 is a cold-shock-inducible protein.
Length = 76
Score = 52.2 bits (126), Expect = 2e-08
Identities = 22/75 (29%), Positives = 47/75 (62%), Gaps = 3/75 (4%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
+EG V VK+I D GA++ L G I+G++ +++++ RR++ +++ +G+ K++
Sbjct: 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61
Query: 1312 KYDQEKNRVSLGMKQ 1326
+ D+EK + L K+
Sbjct: 62 RVDKEKGYIDLSKKR 76
Score = 44.9 bits (107), Expect = 9e-06
Identities = 17/72 (23%), Positives = 40/72 (55%), Gaps = 7/72 (9%)
Query: 1346 LGKVTNLTDYGAFVEIE--KGIEGLVHISEMD--WINKNVTPSKIVQLNDTVEIMILEIN 1401
+ V ++ D GA+V + IEG++ +SE+ I +++ K+V++ + ++ ++
Sbjct: 8 VVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRI-RSI--RKLVKVGRKEVVKVIRVD 64
Query: 1402 EERRRISLGMKQ 1413
+E+ I L K+
Sbjct: 65 KEKGYIDLSKKR 76
Score = 37.2 bits (87), Expect = 0.005
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 15/82 (18%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLS--WTDPGEEIIRNFKK----GD 1478
++GE + +KSI D G ++ L GNI+G+I LS+LS IR+ +K G
Sbjct: 2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRR-------IRSIRKLVKVGR 54
Query: 1479 EIEAIILSIDVEKERISLGIKQ 1500
+ ++ +D EK I L K+
Sbjct: 55 KEVVKVIRVDKEKGYIDLSKKR 76
Score = 29.1 bits (66), Expect = 2.9
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 1514 DKGSLVNGIIKSIDTNKGAIIQLS--NEVEGYLRISEEDNKH----EKKLKIGENIDVLT 1567
++G LV +KSI + GA + L +EG + +SE + K +K+G V
Sbjct: 2 EEGELVVVTVKSI-ADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60
Query: 1568 VLIDHKTRYIQLSFKK 1583
+ +D + YI LS K+
Sbjct: 61 IRVDKEKGYIDLSKKR 76
>gnl|CDD|224018 COG1093, SUI2, Translation initiation factor 2, alpha subunit
(eIF-2alpha) [Translation, ribosomal structure and
biogenesis].
Length = 269
Score = 55.8 bits (135), Expect = 5e-08
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 1256 EGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
EG V G VK + DYGA+++L G +G +HI+++A VK+ + + GQ + K+L+
Sbjct: 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLR 70
Query: 1313 YDQEKNRVSLGMK 1325
D ++ + L +K
Sbjct: 71 VDPKRGHIDLSLK 83
Score = 47.7 bits (114), Expect = 2e-05
Identities = 28/85 (32%), Positives = 48/85 (56%), Gaps = 8/85 (9%)
Query: 1338 RYPR-GTRLLGKVTNLTDYGAFVEIEK--GIEGLVHISEMD--WINKNVTPSKIVQLNDT 1392
YP G ++G V + DYGA+VE+++ G EG +HISE+ W+ KN+ V+
Sbjct: 7 EYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWV-KNI--RDYVKEGQK 63
Query: 1393 VEIMILEINEERRRISLGMKQCKDN 1417
V +L ++ +R I L +K+ ++
Sbjct: 64 VVAKVLRVDPKRGHIDLSLKRVTEH 88
Score = 36.5 bits (85), Expect = 0.080
Identities = 22/80 (27%), Positives = 44/80 (55%), Gaps = 15/80 (18%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLS--WTDPGEEIIRNF----KKGDE 1479
+GE + G +K + D+G ++ LD +G IH+S+++ W ++N K+G +
Sbjct: 11 EGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGW-------VKNIRDYVKEGQK 63
Query: 1480 IEAIILSIDVEKERISLGIK 1499
+ A +L +D ++ I L +K
Sbjct: 64 VVAKVLRVDPKRGHIDLSLK 83
Score = 32.3 bits (74), Expect = 2.0
Identities = 30/94 (31%), Positives = 49/94 (52%), Gaps = 11/94 (11%)
Query: 1168 ESGEIITGTINGKVKG-GLTVLTN---GLKAFLPGSLVDIRPVKDTTPF--EGKTMDFKV 1221
E GEI+ GT+ +V G V + G + F+ S V VK+ + EG+ + KV
Sbjct: 10 EEGEIVVGTVK-QVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKV 68
Query: 1222 IKLDRKRNNVVLSHRAVIEESMGEERQKLIETLK 1255
+++D KR ++ LS + V E +R+K I+ K
Sbjct: 69 LRVDPKRGHIDLSLKRVTE----HQRRKKIQEWK 98
>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain. RNase
R is a processive 3' to 5' exoribonuclease, which is a
homolog of RNase II. RNase R degrades RNA with secondary
structure having a 3' overhang of at least 7 nucleotides.
RNase R and PNPase play an important role in the
degradation of RNA with extensive secondary structure,
such as rRNA, tRNA, and certain mRNA which contains
repetitive extragenic palindromic sequences. The
C-terminal S1 domain binds ssRNA.
Length = 83
Score = 48.6 bits (117), Expect = 5e-07
Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 11/79 (13%)
Query: 1342 GTRLLGKVTNLTDYGAFVEI-EKGIEGLVHISEM--DW---INKNVT-----PSKIVQLN 1390
G G ++ +T +G FVE+ +EGLVH+S + D+ +N K+ +L
Sbjct: 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLG 61
Query: 1391 DTVEIMILEINEERRRISL 1409
D V++ ++ ++ +RR+I
Sbjct: 62 DKVKVRVVRVDLDRRKIDF 80
Score = 45.5 bits (109), Expect = 6e-06
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 19/83 (22%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGN-IDGLIHLSDLSWTDPGEE----------IIRNFKK- 1476
GE+ G+I +T FG+F+ LD ++GL+H+S L + + K
Sbjct: 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTL----GDDYYEFDEENHALVGERTGKV 57
Query: 1477 ---GDEIEAIILSIDVEKERISL 1496
GD+++ ++ +D+++ +I
Sbjct: 58 FRLGDKVKVRVVRVDLDRRKIDF 80
Score = 33.9 bits (79), Expect = 0.069
Identities = 10/34 (29%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 1257 GCTVKGVVKNITDYGAFIDLG--GIDGLLHITDI 1288
G GV+ +T +G F++L ++GL+H++ +
Sbjct: 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTL 35
>gnl|CDD|240191 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain.
pNO40 is a nucleolar protein of unknown function with an
N-terminal S1 RNA binding domain, a CCHC type zinc
finger, and clusters of basic amino acids representing a
potential nucleolar targeting signal. pNO40 was
identified through a yeast two-hybrid interaction screen
of a human kidney cDNA library using the pinin (pnn)
protein as bait. pNO40 is thought to play a role in
ribosome maturation and/or biogenesis.
Length = 73
Score = 47.1 bits (112), Expect = 1e-06
Identities = 21/67 (31%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 1261 KGVVKNITDYGAFIDLGGI--DGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKN 1318
KG V ++T+YGAF+ + G GL+H + ++ RV PSE++ +G+ + K++ + K+
Sbjct: 8 KGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR-EMKD 66
Query: 1319 RVSLGMK 1325
++ L +
Sbjct: 67 KMKLSLS 73
Score = 38.2 bits (89), Expect = 0.002
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 7/71 (9%)
Query: 1345 LLGKVTNLTDYGAFVEIEKGI--EGLVHISEMDWINKNV-TPSKIVQLNDTVEIMILEIN 1401
G+V ++T+YGAFV+I G +GLVH S M + V PS++V + + V + ++
Sbjct: 7 FKGEVASVTEYGAFVKIP-GCRKQGLVHKSHMS--SCRVDDPSEVVDVGEKVWVKVIGR- 62
Query: 1402 EERRRISLGMK 1412
E + ++ L +
Sbjct: 63 EMKDKMKLSLS 73
Score = 31.3 bits (71), Expect = 0.60
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 1433 KGIIKSITDFGIFIGLDG-NIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIEAIILSID 1488
KG + S+T++G F+ + G GL+H S +S DP E + G+++ ++ +
Sbjct: 8 KGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDV----GEKVWVKVIGRE 63
Query: 1489 VEKERISLGIK 1499
K+++ L +
Sbjct: 64 -MKDKMKLSLS 73
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional.
Length = 120
Score = 47.4 bits (113), Expect = 3e-06
Identities = 23/76 (30%), Positives = 44/76 (57%), Gaps = 11/76 (14%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM-----DWINKNVTPSKIVQLNDTVEIM 1396
G +L G +T + YGAFV +E G GL+HISE+ D I+ +++++ + V +
Sbjct: 4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIH------QLLKVGEEVLVQ 57
Query: 1397 ILEINEERRRISLGMK 1412
+++ +E + SL ++
Sbjct: 58 VVDFDEYTGKASLSLR 73
Score = 46.6 bits (111), Expect = 7e-06
Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
+K G +KG + I YGAF+ L G GL+HI++I + + ++L +G+++ +++
Sbjct: 1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVD 60
Query: 1313 YDQEKNRVSLGMKQL 1327
+D+ + SL ++ L
Sbjct: 61 FDEYTGKASLSLRTL 75
Score = 44.3 bits (105), Expect = 4e-05
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
K G+K+KG I I +G F+ L+ GLIH+S++ T + I + K G+E+ ++
Sbjct: 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIK-TGFIDNIHQLLKVGEEVLVQVVD 60
Query: 1487 IDVEKERISLGIKQLE 1502
D + SL ++ LE
Sbjct: 61 FDEYTGKASLSLRTLE 76
>gnl|CDD|235188 PRK03987, PRK03987, translation initiation factor IF-2 subunit alpha;
Validated.
Length = 262
Score = 49.8 bits (120), Expect = 4e-06
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 3/73 (4%)
Query: 1256 EGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
EG V G VK + D+GAF+ L G +G +HI+++A VK+ + + GQ + K+++
Sbjct: 8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIR 67
Query: 1313 YDQEKNRVSLGMK 1325
D K + L +K
Sbjct: 68 VDPRKGHIDLSLK 80
Score = 41.3 bits (98), Expect = 0.002
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 16/90 (17%)
Query: 1347 GKVTNLTDYGAFVEIEK--GIEGLVHISEM--DWINKNVTPSKIVQLNDTVEIMILEINE 1402
G V + D+GAFV +++ G EG +HISE+ W+ KN+ V+ V ++ ++
Sbjct: 14 GTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWV-KNI--RDHVKEGQKVVCKVIRVDP 70
Query: 1403 ERRRISLGMKQCKDNPWENFSIIHKKGEKI 1432
+ I L +K+ + H++ EKI
Sbjct: 71 RKGHIDLSLKRVNE---------HQRREKI 91
Score = 32.5 bits (75), Expect = 1.6
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 15/79 (18%)
Query: 1429 GEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLS--WTDPGEEIIRNF----KKGDEI 1480
GE + G +K + DFG F+ LD +G IH+S+++ W ++N K+G ++
Sbjct: 9 GELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGW-------VKNIRDHVKEGQKV 61
Query: 1481 EAIILSIDVEKERISLGIK 1499
++ +D K I L +K
Sbjct: 62 VCKVIRVDPRKGHIDLSLK 80
Score = 30.9 bits (71), Expect = 5.2
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 10/91 (10%)
Query: 1168 ESGEIITGTINGKVK--GGLTVLT--NGLKAFLPGSLVDIRPVKDTTPF--EGKTMDFKV 1221
E GE++ GT+ +VK G L G + F+ S V VK+ EG+ + KV
Sbjct: 7 EEGELVVGTVK-EVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKV 65
Query: 1222 IKLDRKRNNVVLSHRAVIEESMGEERQKLIE 1252
I++D ++ ++ LS + V E + R+K+ E
Sbjct: 66 IRVDPRKGHIDLSLKRVNEH---QRREKIQE 93
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one or
the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease RNase
R (Rnr). Its paralog in E. coli and H. influenzae is
designated exoribonuclease II (Rnb). Both are involved in
the degradation of mRNA, and consequently have strong
pleiotropic effects that may be difficult to disentangle.
Both these proteins share domain-level similarity (RNB,
S1) with a considerable number of other proteins, and
full-length similarity scoring below the trusted cutoff
to proteins associated with various phenotypes but
uncertain biochemistry; it may be that these latter
proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 50.1 bits (120), Expect = 8e-06
Identities = 32/136 (23%), Positives = 56/136 (41%), Gaps = 22/136 (16%)
Query: 1379 KNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKK-GEKIKGIIK 1437
K T ++ Q D + + ++ RR + D W + K G + G I
Sbjct: 524 KEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVAD--WLKCRYLLDKVGTEFSGEIS 581
Query: 1438 SITDFGIFIGLDGN-IDGLIHLSDLSWTDPGEEII--------------RNFKKGDEIEA 1482
S+T FG+F+ LD N IDGLIH+S L + + + ++ GD +
Sbjct: 582 SVTRFGMFVRLDDNGIDGLIHISTL----HNDYYVFDQEKMALIGKGTGKVYRIGDRVTV 637
Query: 1483 IILSIDVEKERISLGI 1498
+ +++E I +
Sbjct: 638 KLTEVNMETRSIIFEL 653
Score = 35.8 bits (83), Expect = 0.24
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 15/79 (18%)
Query: 1342 GTRLLGKVTNLTDYGAFVEI-EKGIEGLVHIS------------EMDWINKNVTPSKIVQ 1388
GT G+++++T +G FV + + GI+GL+HIS +M I K K+ +
Sbjct: 573 GTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKG--TGKVYR 630
Query: 1389 LNDTVEIMILEINEERRRI 1407
+ D V + + E+N E R I
Sbjct: 631 IGDRVTVKLTEVNMETRSI 649
>gnl|CDD|215104 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 49.1 bits (117), Expect = 2e-05
Identities = 31/108 (28%), Positives = 53/108 (49%), Gaps = 13/108 (12%)
Query: 1298 EILTIGQDISTKILKYDQEKNRVSLG-MKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYG 1356
E + D + KI D S + L + P +G +R ++ ++ YG
Sbjct: 717 EAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRN-------CEIKSIAPYG 769
Query: 1357 AFVEIEKGIEGLVHISEM--DWINKNVTPSKIVQLNDTVEIMILEINE 1402
AFVEI G EGL HISE+ +W+ K P ++ D +++ ++E+N+
Sbjct: 770 AFVEIAPGREGLCHISELSSNWLAK---PEDAFKVGDRIDVKLIEVND 814
Score = 36.8 bits (85), Expect = 0.11
Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 1264 VKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSL 1322
+K+I YGAF+++ G +GL HI++++ + P + +G I K+++ + +K ++ L
Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRL 820
Query: 1323 GMKQLGIDP 1331
+ L +
Sbjct: 821 SRRALLPEA 829
Score = 36.8 bits (85), Expect = 0.13
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 1436 IKSITDFGIFIGLDGNIDGLIHLSDLS--WTDPGEEIIRNFKKGDEIEAIILSIDVEKER 1493
IKSI +G F+ + +GL H+S+LS W E+ FK GD I+ ++ ++ +K +
Sbjct: 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA---FKVGDRIDVKLIEVN-DKGQ 817
Query: 1494 ISLGIKQLEGDP 1505
+ L + L +
Sbjct: 818 LRLSRRALLPEA 829
>gnl|CDD|240212 cd05707, S1_Rrp5_repeat_sc11, S1_Rrp5_repeat_sc11: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 68
Score = 42.7 bits (101), Expect = 4e-05
Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAI----I 1484
G+ ++G +K+I + G+F+ L +D + +S+LS + ++++KK ++ + I
Sbjct: 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELS-----DSYLKDWKKRFKVGQLVKGKI 55
Query: 1485 LSIDVEKERISL 1496
+SID + RI +
Sbjct: 56 VSIDPDNGRIEM 67
Score = 42.3 bits (100), Expect = 6e-05
Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 1257 GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G V+G VKNI + G F+ LG G+D + +++++ +K + +GQ + KI+ D
Sbjct: 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDP 60
Query: 1316 EKNRVSL 1322
+ R+ +
Sbjct: 61 DNGRIEM 67
Score = 33.0 bits (76), Expect = 0.12
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 13/69 (18%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISE------MDWINKNVTPSKIVQLNDTVEIMILEI 1400
G V N+ + G FV + +G++ V +SE DW + ++ V+ I+ I
Sbjct: 6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKR-------FKVGQLVKGKIVSI 58
Query: 1401 NEERRRISL 1409
+ + RI +
Sbjct: 59 DPDNGRIEM 67
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli and
is broadly distributed throughout the bacteria. In E.
coli, double mutants of this protein and polynucleotide
phosphorylase are not viable. Scoring between trusted and
noise cutoffs to the model are shorter, divergent forms
from the Chlamydiae, and divergent forms from the
Campylobacterales (including Helicobacter pylori) and
Leptospira interrogans [Transcription, Degradation of
RNA].
Length = 709
Score = 47.6 bits (114), Expect = 5e-05
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 11/77 (14%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGN-IDGLIHLSDLS----WTDP------GEEIIRNFKKG 1477
GE+ +G+I +T FG+F+ L+ N I+GL+H+S L D GE + F+ G
Sbjct: 628 GEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLG 687
Query: 1478 DEIEAIILSIDVEKERI 1494
D ++ ++ D++ +I
Sbjct: 688 DRVKVRVVKADLDTGKI 704
Score = 43.8 bits (104), Expect = 7e-04
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIE-KGIEGLVHISEMD-----WINKNVTPS-----KIVQLN 1390
G G ++ +T +G FVE+E IEGLVHIS + + K + K+ +L
Sbjct: 628 GEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLG 687
Query: 1391 DTVEIMILEINEERRRI 1407
D V++ +++ + + +I
Sbjct: 688 DRVKVRVVKADLDTGKI 704
Score = 35.7 bits (83), Expect = 0.26
Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 1257 GCTVKGVVKNITDYGAFIDL--GGIDGLLHITDI 1288
G +GV+ +T +G F++L I+GL+HI+ +
Sbjct: 628 GEEFEGVISGVTSFGLFVELENNTIEGLVHISTL 661
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 44.2 bits (105), Expect = 1e-04
Identities = 52/220 (23%), Positives = 86/220 (39%), Gaps = 65/220 (29%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
VITI G SGK TVA+ +A LG + +G ++R ++ E + +
Sbjct: 2 VITISGLPGSGKTTVARELAEHLGLKLVSAGTIFR-----------EMARERGMSLE--- 47
Query: 921 LNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIA-KFKNIRKELFKIQVKFRKFPGLVAD 979
S+ A + I KE+ + Q + K +V +
Sbjct: 48 ----------------------------EFSRYAEEDPEIDKEIDRRQKELAKEGNVVLE 79
Query: 980 GRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTR- 1038
GR G V A LKI+L A ++ R +R + K + + + L ++R+ +K R
Sbjct: 80 GRLAGWIVREYADLKIWLKAPLEVRAER-----IAKREGIDVDEALAETVEREESEKKRY 134
Query: 1039 ---------NLSPLKCPEQAHL-LNTSKMNINQVVNQILD 1068
+LS L +NTSK + +V +LD
Sbjct: 135 KKIYGIDIDDLS------IYDLVINTSKWDPEEVFLILLD 168
>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. RpoE is subunit E of archaeal
RNA polymerase. Archaeal cells contain a single RNA
polymerase made up of 12 subunits, which are homologous
to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase
II. RpoE is homologous to Rpa43 of eukaryotic RNA
polymerase I, RPB7 of eukaryotic RNA polymerase II, and
Rpc25 of eukaryotic RNA polymerase III. RpoE is composed
of two domains, the N-terminal RNP (ribonucleoprotein)
domain and the C-terminal S1 domain. This S1 domain binds
ssRNA and ssDNA. This family is classified based on the
C-terminal S1 domain. The function of RpoE is not fully
understood. In eukaryotes, RPB7 and RPB4 form a
heterodimer that reversibly associates with the RNA
polymerase II core.
Length = 99
Score = 42.3 bits (100), Expect = 1e-04
Identities = 32/93 (34%), Positives = 53/93 (56%), Gaps = 9/93 (9%)
Query: 1260 VKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKH-PSEILTIGQDISTKILKY-DQEK 1317
V+G V + D+GAF+ +G +DGLLHI+ I + + P IG++ + ++LK D +
Sbjct: 3 VEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEE-TKRVLKVGDVVR 61
Query: 1318 NR-VSLGMKQLGI-DPWIGLSFRYPRGTRLLGK 1348
R V++ +K+ + IGL+ R P LGK
Sbjct: 62 ARIVAVSLKERRPRESKIGLTMRQP----GLGK 90
Score = 40.7 bits (96), Expect = 5e-04
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 11/78 (14%)
Query: 1430 EKIKGIIKSITDFGIFIGLDGNIDGLIHLS----DLSWTDP------GEEIIRNFKKGDE 1479
E ++G + + DFG F+ + G +DGL+H+S D DP GEE R K GD
Sbjct: 1 EVVEGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDV 59
Query: 1480 IEAIILSIDVEKERISLG 1497
+ A I+++ +++ R
Sbjct: 60 VRARIVAVSLKERRPRES 77
Score = 33.0 bits (76), Expect = 0.25
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 16/82 (19%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISE-----MDWINKNVT-----PSKIVQLNDTV--E 1394
G+V + D+GAFV I ++GL+HIS+ + + KN +++++ D V
Sbjct: 5 GEVVEVVDFGAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRAR 63
Query: 1395 IMILEINEERR---RISLGMKQ 1413
I+ + + E R +I L M+Q
Sbjct: 64 IVAVSLKERRPRESKIGLTMRQ 85
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 44.0 bits (105), Expect = 2e-04
Identities = 14/29 (48%), Positives = 22/29 (75%)
Query: 1260 VKGVVKNITDYGAFIDLGGIDGLLHITDI 1288
V+G V + ++GAF+ +G +DGLLHI+ I
Sbjct: 85 VEGEVVEVVEFGAFVRIGPVDGLLHISQI 113
Score = 42.1 bits (100), Expect = 6e-04
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 20/89 (22%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDP------------GEEIIRNFKK 1476
E ++G + + +FG F+ + G +DGL+H+S + D G+E R K
Sbjct: 82 QEVVEGEVVEVVEFGAFVRI-GPVDGLLHISQI--MDDYISYDPKNGRLIGKESKRVLKV 138
Query: 1477 GDEIEAII--LSIDVEKER---ISLGIKQ 1500
GD + A I +S+ + R I L ++Q
Sbjct: 139 GDVVRARIVAVSLKERRPRGSKIGLTMRQ 167
Score = 37.5 bits (88), Expect = 0.023
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 18/83 (21%)
Query: 1347 GKVTNLTDYGAFVEIEKG-IEGLVHISE-----MDWINKNVT-----PSKIVQLNDTVEI 1395
G+V + ++GAFV I G ++GL+HIS+ + + KN +++++ D V
Sbjct: 87 GEVVEVVEFGAFVRI--GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRA 144
Query: 1396 MI--LEINEERRR---ISLGMKQ 1413
I + + E R R I L M+Q
Sbjct: 145 RIVAVSLKERRPRGSKIGLTMRQ 167
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 43.3 bits (103), Expect = 2e-04
Identities = 56/229 (24%), Positives = 91/229 (39%), Gaps = 64/229 (27%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
+ITI GP SGK TVA+L+A KLG ++ +G ++R EL K+
Sbjct: 2 IITISGPPGSGKTTVARLLAEKLGLKHVSAGEIFR-----------------ELA---KE 41
Query: 921 LNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKF-RKFPGLVAD 979
+ E N+ + I KE+ + Q++ K +V +
Sbjct: 42 RGMSLE--EF------------NKYAEED-------PEIDKEIDRRQLEIAEKEDNVVLE 80
Query: 980 GRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTR- 1038
GR G A LKI+L A ++ R +R + + +S+ + L I+R+ + R
Sbjct: 81 GRLAGWMAKDYADLKIWLKAPLEVRAER-----IAEREGISVEEALEETIEREESEAKRY 135
Query: 1039 ---------NLSPLKCPEQAHL-LNTSKMNINQVVNQILDCFATLFKES 1077
+LS L +NTS+ + V + IL L K
Sbjct: 136 KEYYGIDIDDLSI------YDLVINTSRWDPEGVFDIILTAIDKLLKAK 178
>gnl|CDD|239919 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the
archaea-specific RecJ-like exonuclease. The function of
this family is not fully understood. In Escherichia coli,
RecJ degrades single-stranded DNA in the 5'-3' direction
and participates in homologous recombination and mismatch
repair.
Length = 77
Score = 40.7 bits (96), Expect = 3e-04
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLND 1391
GKV + YG FV++ + GL+H S + + V IVQ+ D
Sbjct: 22 GKVNGVAKYGVFVDLNDHVRGLIHRSNLL-RDYEVGDEVIVQVTD 65
Score = 38.7 bits (91), Expect = 0.001
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 9/53 (16%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEI 1480
G+ KG + + +G+F+ L+ ++ GLIH S+L +R+++ GDE+
Sbjct: 16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL---------LRDYEVGDEV 59
Score = 34.9 bits (81), Expect = 0.033
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 1251 IETLKEGCTVKGVVKNITDYGAFIDLGG-IDGLLH 1284
+E L+ G KG V + YG F+DL + GL+H
Sbjct: 11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIH 45
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 45.1 bits (107), Expect = 3e-04
Identities = 28/112 (25%), Positives = 49/112 (43%), Gaps = 12/112 (10%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G+ KGI+ + +G+F+ L+ ++ GLIH DL ++ GDEI + +
Sbjct: 123 GKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-------PDYAVGDEIIVQVSDVR 175
Query: 1489 VEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEV 1540
EK I L+ Y + + L +I +D G +++ EV
Sbjct: 176 PEKGEIDFEPVGLDR-----YREVQVEKELPRTLIDDLDEMIGKTVRIEGEV 222
Score = 32.4 bits (74), Expect = 2.7
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEM-DWINKNVTPSKIVQLNDT 1392
G V+ + YG FVE+ + GL+H ++ + V IVQ++D
Sbjct: 128 GIVSRVEKYGVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDV 174
>gnl|CDD|240203 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat
5 (sc5). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 70
Score = 40.3 bits (95), Expect = 3e-04
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM--DWINKNVTPSKIVQLNDTVEIMILE 1399
G + G + + G V ++G + SE+ +I P + ++ V++ +L
Sbjct: 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKD---PEEHFRVGQVVKVKVLS 57
Query: 1400 INEERRRISLGMK 1412
+ E++R+ L K
Sbjct: 58 CDPEQQRLLLSCK 70
Score = 38.0 bits (89), Expect = 0.002
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSID 1488
G K G I + G + N+ G + S+LS ++ +F+ G ++ +LS D
Sbjct: 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELS-EAFIKDPEEHFRVGQVVKVKVLSCD 59
Query: 1489 VEKERISLGIK 1499
E++R+ L K
Sbjct: 60 PEQQRLLLSCK 70
Score = 37.2 bits (87), Expect = 0.004
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 1262 GVVKNITDYGAFID-LGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
G + + G + + G L ++++ +K P E +GQ + K+L D E+ R+
Sbjct: 6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65
Query: 1321 SLGMK 1325
L K
Sbjct: 66 LLSCK 70
Score = 31.4 bits (72), Expect = 0.40
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYL---RISEED-NKHEKKLKIGENIDVLTVLID 1571
G +G I + N G I+ N V+G+L +SE E+ ++G+ + V + D
Sbjct: 1 GLKTHGTIVKVKPN-GCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCD 59
Query: 1572 HKTRYIQLSFK 1582
+ + + LS K
Sbjct: 60 PEQQRLLLSCK 70
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 42.7 bits (101), Expect = 5e-04
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 13/80 (16%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLS----------WTDPGEEIIRNFKKG 1477
+GE ++G + + +FG F+ + G +DGL+H+S + GEE R K G
Sbjct: 81 RGEVVEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVG 139
Query: 1478 DEIEAII--LSIDVEKERIS 1495
D++ A I +S+ + R S
Sbjct: 140 DKVRARIVGVSLKSRRPRES 159
Score = 36.5 bits (85), Expect = 0.047
Identities = 22/92 (23%), Positives = 45/92 (48%), Gaps = 18/92 (19%)
Query: 1260 VKGVVKNITDYGAFIDLGGIDGLLHITDI----------AWRRVKHPSE-ILTIGQDIST 1308
V+G V + ++GAF+ +G +DGL+H++ I + ++ +L +G +
Sbjct: 85 VEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRA 144
Query: 1309 KILKYD-----QEKNRVSLGMKQ--LGIDPWI 1333
+I+ ++++ L M+Q LG WI
Sbjct: 145 RIVGVSLKSRRPRESKIGLTMRQPGLGKLEWI 176
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 44.4 bits (105), Expect = 5e-04
Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 7/65 (10%)
Query: 1263 VVKNITDYGAFIDL-GGIDGLLHITDI----AWRRVKHPSEILTIGQDISTKILKYDQEK 1317
VVK T +GAF+ L G DGLLHI+ I +RV++ ++L++GQ I +I D ++
Sbjct: 655 VVKT-TAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID-DR 712
Query: 1318 NRVSL 1322
++SL
Sbjct: 713 GKLSL 717
Score = 44.4 bits (105), Expect = 5e-04
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWIN--KNVTP-SKIVQLNDTVEIMIL 1398
G R LG V T +GAFV + G +GL+HIS++ + K V ++ + +++ I
Sbjct: 648 GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIA 707
Query: 1399 EINEERRRISL 1409
+I ++R ++SL
Sbjct: 708 DI-DDRGKLSL 717
Score = 32.5 bits (74), Expect = 2.1
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPG---EEIIRNFKKGDEIEAIIL 1485
GE+ G + T FG F+ L DGL+H+S + G E + G +I+ I
Sbjct: 648 GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIA 707
Query: 1486 SIDVEKERISL 1496
ID ++ ++SL
Sbjct: 708 DID-DRGKLSL 717
>gnl|CDD|240210 cd05705, S1_Rrp5_repeat_hs14, S1_Rrp5_repeat_hs14: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 14 (hs14). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 74
Score = 38.9 bits (91), Expect = 0.001
Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEE--IIRNFKKGDEIEAII 1484
K+G+ ++G + S+T G+F L +I G + +++ + + +G + A +
Sbjct: 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKV 61
Query: 1485 LSIDVEKERISL 1496
LS++ EK + L
Sbjct: 62 LSVNSEKNLVEL 73
Score = 33.1 bits (76), Expect = 0.11
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPS---EILTIGQDISTK 1309
+KEG ++G V ++T G F L I G + ++ V PS + L G+ ++ K
Sbjct: 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAK 60
Query: 1310 ILKYDQEKNRVSL 1322
+L + EKN V L
Sbjct: 61 VLSVNSEKNLVEL 73
>gnl|CDD|240211 cd05706, S1_Rrp5_repeat_sc10, S1_Rrp5_repeat_sc10: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in
eukaryotes but not in prokaryotes or archaea.
Length = 73
Score = 38.8 bits (91), Expect = 0.001
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEM--DWINKNVTPSKIVQLNDTVEIMILE 1399
G L G+VT + D V++ + G I++ D+ K ND V +L
Sbjct: 4 GDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKK---NDIVRACVLS 60
Query: 1400 INEERRRISL 1409
++ ++I+L
Sbjct: 61 VDVPNKKIAL 70
Score = 35.7 bits (83), Expect = 0.013
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
K G+ + G + + D + + L + G ++D D E + FKK D + A +LS
Sbjct: 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDAL-DDYSEALPYKFKKNDIVRACVLS 60
Query: 1487 IDVEKERISL 1496
+DV ++I+L
Sbjct: 61 VDVPNKKIAL 70
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 43.1 bits (102), Expect = 0.001
Identities = 28/132 (21%), Positives = 57/132 (43%), Gaps = 30/132 (22%)
Query: 1387 VQLNDTVEIMILEINE-ERR-----RISLGMKQC---KDNPWENFSIIHKKGEKIKGIIK 1437
+ ++ + I+ ERR R + + + K E F G++
Sbjct: 582 KTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEF----------DGVVT 631
Query: 1438 SITDFGIFIGLDGN-IDGLIHLSDLSWT----DP------GEEIIRNFKKGDEIEAIILS 1486
+T FG F+ L ++GL+H+S L D GE+ + ++ GDE++ + S
Sbjct: 632 GVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTS 691
Query: 1487 IDVEKERISLGI 1498
+D+++ +I +
Sbjct: 692 VDLDERKIDFEL 703
Score = 42.4 bits (100), Expect = 0.002
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 11/81 (13%)
Query: 1342 GTRLLGKVTNLTDYGAFVEI-EKGIEGLVHISEMD----------WINKNVTPSKIVQLN 1390
G G VT +T +G FVE+ E G+EGLVHIS + K+ +L
Sbjct: 623 GEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLG 682
Query: 1391 DTVEIMILEINEERRRISLGM 1411
D V++ + ++ + R+I +
Sbjct: 683 DEVKVKVTSVDLDERKIDFEL 703
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 41.7 bits (98), Expect = 0.004
Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 11/77 (14%)
Query: 1429 GEKIKGIIKSITDFGIFIGL-DGNIDGLIHLSDLS-----WTDPGEEII-----RNFKKG 1477
G KG+I S+T FG F+ L D IDGL+H+S L + G+ +I + ++ G
Sbjct: 644 GNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLG 703
Query: 1478 DEIEAIILSIDVEKERI 1494
D +E + ++++++ +I
Sbjct: 704 DRVEVRVEAVNMDERKI 720
Score = 32.8 bits (75), Expect = 2.1
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 1342 GTRLLGKVTNLTDYGAFVEI-EKGIEGLVHISEMD---WINKNV-------TPSKIVQLN 1390
G G ++++T +G FV + + I+GLVH+S +D + V + + +L
Sbjct: 644 GNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLG 703
Query: 1391 DTVEIMILEINEERRRI 1407
D VE+ + +N + R+I
Sbjct: 704 DRVEVRVEAVNMDERKI 720
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 39.3 bits (92), Expect = 0.005
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
+ITI GP SGK TVA+++A KL + +G ++R
Sbjct: 2 IITISGPPGSGKTTVAKILAEKLSLKLISAGDIFR 36
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is
a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner mitochondrial
membrane. The main function of the complex is to
transport electrons from NADH to ubiquinone, which is
accompanied by the translocation of protons from the
mitochondrial matrix to the inter membrane space.
Length = 219
Score = 40.0 bits (94), Expect = 0.005
Identities = 20/38 (52%), Positives = 24/38 (63%), Gaps = 8/38 (21%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGF--------HYLDS 890
VIT+DG ASGKG +A+ +A KLG HYLDS
Sbjct: 1 VITVDGNIASGKGKLAKELAEKLGMKYFPEAGIHYLDS 38
>gnl|CDD|240207 cd05702, S1_Rrp5_repeat_hs11_sc8, S1_Rrp5_repeat_hs11_sc8: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1
repeat 8 (sc8). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 70
Score = 35.3 bits (82), Expect = 0.020
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDL--SWTDPGEEIIRNFKKGDEIEAIIL 1485
G+ +K +KS+ + + L N+ G IH+S++ W D G+ + FK G +I+A ++
Sbjct: 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPD-GKNPLSKFKIGQKIKARVI 58
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 37.3 bits (87), Expect = 0.028
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
I I GP +GK T+A+ +A KLG +LD+G + R
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKLGLPHLDTGDILR 36
>gnl|CDD|236410 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 37.9 bits (89), Expect = 0.041
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 1425 IHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAII 1484
+ GE I G++K + I + L G + ++ + P E NF+ GD + A +
Sbjct: 131 KDRVGEIITGVVKRVERGNIIVDL-GRAEAILPRKEQI---PRE----NFRPGDRVRAYV 182
Query: 1485 LSIDVEKE 1492
+V KE
Sbjct: 183 Y--EVRKE 188
Score = 31.4 bits (72), Expect = 4.8
Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 21/112 (18%)
Query: 1098 RNFVIINADLKSEAFIPIEEFKNDNGELEVKIGDFVSVAIESLENGFG--------DTIL 1149
R + ++ I +EE + + + ++GD++ IES++ FG I+
Sbjct: 60 RRWEVVEEVEDPTKEISLEEARKIDPD--AEVGDYIEEEIESVD--FGRIAAQTAKQVIV 115
Query: 1150 SR----DKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLTNGLKAFLP 1197
+ ++ + + GEIITG + +G + V +A LP
Sbjct: 116 QKIREAERERVYEEYKDRV-----GEIITGVVKRVERGNIIVDLGRAEAILP 162
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 36.1 bits (84), Expect = 0.046
Identities = 15/51 (29%), Positives = 29/51 (56%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNE 911
+I + G + SGK TV + +A +LG ++D L+ ++ + I L++E
Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAPFIDGDDLHPPANIAKMAAGIPLNDE 51
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 36.8 bits (86), Expect = 0.049
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP SGKGT A+ +A K G ++ +G L R
Sbjct: 6 GPPGSGKGTQAKRIAEKYGLPHISTGDLLR 35
>gnl|CDD|221968 pfam13189, Cytidylate_kin2, Cytidylate kinase-like family. This
family includes enzymes related to cytidylate kinase.
Length = 176
Score = 36.4 bits (85), Expect = 0.054
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDS 890
+ITI SG + + +A KLG Y D
Sbjct: 1 IITISRQFGSGGREIGKKLAEKLGIPYYDR 30
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 36.4 bits (85), Expect = 0.056
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYL 888
VI ++G +GK T+A+ +A LG+ +
Sbjct: 1 VIVVEGNIGAGKSTLAKELAEHLGYEVV 28
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and
eukaryotic form. This family seems to be confined to the
archea and eukaryotic taxa and are quite dissimilar to
E.coli rpoE [Transcription, DNA-dependent RNA
polymerase].
Length = 179
Score = 36.3 bits (84), Expect = 0.059
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 11/77 (14%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLS----DLSWTDP------GEEIIRNFKKGD 1478
GE ++G + I +FG F+ L G DGL H+S D + DP G+E + +GD
Sbjct: 82 GEIVEGEVIEIVEFGAFVSL-GPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGD 140
Query: 1479 EIEAIILSIDVEKERIS 1495
++ A I+++ ++ R
Sbjct: 141 KVRARIVALSLKDRRPE 157
Score = 30.9 bits (70), Expect = 3.5
Identities = 13/29 (44%), Positives = 20/29 (68%)
Query: 1260 VKGVVKNITDYGAFIDLGGIDGLLHITDI 1288
V+G V I ++GAF+ LG DGL H++ +
Sbjct: 85 VEGEVIEIVEFGAFVSLGPFDGLFHVSQV 113
>gnl|CDD|225685 COG3143, CheZ, Chemotaxis protein [Cell motility and secretion /
Signal transduction mechanisms].
Length = 217
Score = 35.9 bits (83), Expect = 0.099
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 11/75 (14%)
Query: 482 VIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNA--INPSTEDLI 539
VIK+V+D+ + +++ I+ D N +++ R + +LN +NPS D++
Sbjct: 151 VIKRVMDVVQEIE--SQLVMILLD--NAPEHE----SAPKRENASLLNGPQVNPSKADVV 202
Query: 540 ASQDMVIT-LSNLGY 553
ASQD V L +LG+
Sbjct: 203 ASQDQVDDLLDSLGF 217
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 35.3 bits (82), Expect = 0.13
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVI 916
GP SGKGT A+ +A K G ++ +G L R I + +L + + I
Sbjct: 6 GPPGSGKGTQAERLAKKYGLPHISTGDLLR----EEIASGTELGKKAKEYI 52
>gnl|CDD|239902 cd04455, S1_NusA, S1_NusA: N-utilizing substance A protein (NusA),
S1-like RNA-binding domain. S1-like RNA-binding domains
are found in a wide variety of RNA-associated proteins.
NusA is a transcription elongation factor containing an
N-terminal catalytic domain and three RNA binding domains
(RBD's). The RBD's include one S1 domain and two KH
domains that form an RNA binding surface. DNA
transcription by RNA polymerase (RNAP) includes three
phases - initiation, elongation, and termination. During
initiation, sigma factors bind RNAP and target RNAP to
specific promoters. During elongation, N-utilization
substances (NusA, B, E, and G) replace sigma factors and
regulate pausing, termination, and antitermination. NusA
is cold-shock-inducible.
Length = 67
Score = 32.4 bits (75), Expect = 0.16
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 10/66 (15%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
++GE + GI+K + + + L G ++ ++ + PGE +++ GD I+A +L
Sbjct: 2 REGEIVTGIVKRVDRGNVIVDL-GKVEAILPKKEQI---PGE----SYRPGDRIKAYVL- 52
Query: 1487 IDVEKE 1492
+V K
Sbjct: 53 -EVRKT 57
Score = 30.5 bits (70), Expect = 0.86
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 1084 RSGEVISAEVIGLDRNFVIINADLKSEAFIPIEE 1117
R GE+++ V +DR VI++ K EA +P +E
Sbjct: 2 REGEIVTGIVKRVDRGNVIVDLG-KVEAILPKKE 34
>gnl|CDD|201213 pfam00406, ADK, Adenylate kinase.
Length = 186
Score = 34.6 bits (80), Expect = 0.25
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A+ + K G +L +G L R
Sbjct: 3 GPPGAGKGTQAERIVQKYGIPHLSTGDLLR 32
>gnl|CDD|237746 PRK14529, PRK14529, adenylate kinase; Provisional.
Length = 223
Score = 34.7 bits (80), Expect = 0.29
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
I I GP SGKGT LV K +++SGA++R
Sbjct: 3 ILIFGPNGSGKGTQGALVKKKYDLAHIESGAIFR 36
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 31.9 bits (73), Expect = 0.30
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 861 VITIDGPTASGKGTVAQLVASKLG---FHYLDSGALY 894
+I I G + SGK TVA+ +A +LG LD +
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGGRSVVVLDEIVIL 37
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 33.9 bits (78), Expect = 0.31
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 859 IPVITIDGPTASGKGTVAQLVASKLGF 885
+ + IDG + SGK T+A +A++ GF
Sbjct: 15 MITVLIDGRSGSGKTTLAGALAARTGF 41
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 33.7 bits (77), Expect = 0.47
Identities = 16/51 (31%), Positives = 34/51 (66%), Gaps = 4/51 (7%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVI 916
GP SGKGT+A++++++L ++++ +G L+R I N+ L E++ ++
Sbjct: 7 GPPGSGKGTIAKILSNELNYYHISTGDLFR----ENILNSTPLGKEIKQIV 53
>gnl|CDD|130427 TIGR01360, aden_kin_iso1, adenylate kinase, isozyme 1 subfamily.
Members of this family are adenylate kinase, EC 2.7.4.3.
This clade is found only in eukaryotes and includes
human adenylate kinase isozyme 1 (myokinase). Within the
adenylate kinase superfamily, this set appears
specifically closely related to a subfamily of
eukaryotic UMP-CMP kinases (TIGR01359), rather than to
the large clade of bacterial, archaeal, and eukaryotic
adenylate kinase family members in TIGR01351.
Length = 188
Score = 33.3 bits (76), Expect = 0.62
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 857 KYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
+I I G SGKGT + + K GF +L +G L R
Sbjct: 1 AKCKIIFIVGGPGSGKGTQCEKIVEKYGFTHLSTGDLLR 39
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 32.8 bits (75), Expect = 0.84
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLD 889
+ G SGK T+A +A +LG +++
Sbjct: 1 FVLMGVAGSGKSTIASALAHRLGAKFIE 28
>gnl|CDD|240208 cd05703, S1_Rrp5_repeat_hs12_sc9, S1_Rrp5_repeat_hs12_sc9: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1
repeat 9 (sc9). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 73
Score = 30.6 bits (70), Expect = 0.95
Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPG--EEIIRNFKKGDEIEAIILS 1486
G+++ G + +++ +++ + ++ G I L DLS D E + F G ++A ++
Sbjct: 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLS-DDVSVLEHPEKKFPIGQALKAKVVG 59
Query: 1487 IDVEKERISL 1496
+D E + + L
Sbjct: 60 VDKEHKLLRL 69
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 32.1 bits (74), Expect = 1.3
Identities = 11/31 (35%), Positives = 21/31 (67%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDS 890
P I + G +GK T+ +L+A +LG+ ++D+
Sbjct: 5 PNIVLIGFMGAGKSTIGRLLAKRLGYDFIDT 35
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 31.9 bits (73), Expect = 1.3
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLD 889
G + SGK TV +A +LG ++D
Sbjct: 2 GVSGSGKSTVGSALAERLGAKFID 25
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.3 bits (71), Expect = 1.5
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLD 889
I I G SGK T+A+ +A +LG D
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRD 28
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 32.2 bits (74), Expect = 1.8
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 6/76 (7%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPS----EILTIGQDISTK 1309
K G V G V ++T G +D+ L ++++ R V + L IG I K
Sbjct: 62 KVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAK 121
Query: 1310 ILKYDQEKNRVSLGMK 1325
+ D V L +K
Sbjct: 122 VKDVD-RTRDVVLTLK 136
>gnl|CDD|149583 pfam08581, Tup_N, Tup N-terminal. The N-terminal domain of the Tup
protein has been shown to interact with the Ssn6
transcriptional co-repressor.
Length = 79
Score = 29.6 bits (67), Expect = 2.1
Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 428 KKNYNTISKINNISKLQNNDM-YKLSDIQAQEILKMPLQRLTNME--QKKIINKYENVIK 484
+ + +S+ + K Q +D +K+ Q QE ++M Q + +E +K+ KYE I
Sbjct: 10 RAEFEALSREASSYKAQQDDYEHKIQQ-QIQE-MQMIRQTVYELEQAHRKMKQKYEEEIA 67
Query: 485 K 485
+
Sbjct: 68 R 68
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 31.5 bits (72), Expect = 2.4
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLD 889
+ + G GK TV +A LG+ ++D
Sbjct: 5 LFLVGARGCGKTTVGMALAQALGYRFVD 32
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 31.0 bits (71), Expect = 2.5
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDS 890
I + G +GK TV +L+A LG ++D
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALGLPFVDL 30
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
with domain III, which is central to the structure of
Thermus aquaticus MutS as characterized in.
Length = 290
Score = 32.0 bits (73), Expect = 2.5
Identities = 27/177 (15%), Positives = 59/177 (33%), Gaps = 10/177 (5%)
Query: 356 LHRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIEST- 414
L + + R + +L R L L L + + P+ + ++E
Sbjct: 82 LLSRLALGRASPRDLLALRSSLEALPALRKLLASAPLLADLADQLPLPELLE--LLERAI 139
Query: 415 -WNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQK 473
+ P + G K Y+ +++ + L + KL+++ +E + ++ L +
Sbjct: 140 DEDPPLSLRDGGVIKDGYD--PELDELRALLDELREKLAELLERERERTGIKSLKVGYNR 197
Query: 474 KIINKYENVIKKVIDLTD----ILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEI 526
V D S +K + T EL ++ K ++ E
Sbjct: 198 VFGYYVIEVKASKADKVPGDYIRRSTTKNAVRFTTPELKELERKLLEAEERALALEK 254
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 32.5 bits (74), Expect = 2.5
Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 5/122 (4%)
Query: 408 NKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRL 467
K E NL + + N K NT+ NNI +N + I+ + +P +
Sbjct: 2363 IKTKEKINNLKEEFSKLLKNIKRNNTLCNNNNIKDFISNIGKSVETIKQRFSSNLPEK-- 2420
Query: 468 TNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEII 527
E+ I + N IK +++ T +SN I +++ KNK ++ + ++I
Sbjct: 2421 ---EKLHQIEENLNEIKNIMNETKRISNVDAFTNKILQDIDNEKNKENNNMNAEKIDDLI 2477
Query: 528 LN 529
N
Sbjct: 2478 EN 2479
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 31.2 bits (71), Expect = 2.7
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 11/78 (14%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
+I I G GK TV++L+A KLG+ Y+D +T A+ I + + E+ I K
Sbjct: 2 IIAITGTPGVGKTTVSKLLAEKLGYEYVD-------LTEFALKKGIGEEKDDEMEIDFDK 54
Query: 921 LNYN----FLGKEVYLNG 934
L Y F K V L+G
Sbjct: 55 LAYFIEEEFKEKNVVLDG 72
>gnl|CDD|239900 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like
RNA-binding domain. RNase E is an essential
endoribonuclease in the processing and degradation of
RNA. In addition to its role in mRNA degradation, RNase E
has also been implicated in the processing of rRNA, and
the maturation of tRNA, 10Sa RNA and the M1 precursor of
RNase P. RNase E associates with PNPase (3' to 5'
exonuclease), Rhl B (DEAD-box RNA helicase) and enolase
(glycolytic enzyme) to form the RNA degradosome. RNase E
tends to cut mRNA within single-stranded regions that are
rich in A/U nucleotides. The N-terminal region of RNase E
contains the catalytic site. Within the conserved
N-terminal domain of RNAse E and RNase G, there is an
S1-like subdomain, which is an ancient single-stranded
RNA-binding domain. S1 domain is an RNA-binding module
originally identified in the ribosomal protein S1. The S1
domain is required for RNA cleavage by RNase E. RNase G
is paralogous to RNase E with an N-terminal catalytic
domain that is highly homologous to that of RNase E.
RNase G not only shares sequence similarity with RNase E,
but also functionally overlaps with RNase E. In
Escherichia coli, RNase G is involved in the maturation
of the 5' end of the 16S rRNA. RNase G plays a secondary
role in mRNA decay.
Length = 88
Score = 29.1 bits (66), Expect = 4.8
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 1515 KGSLVNGIIKSIDTN-KGAIIQLSNEVEGYLRISE-------EDNKHEKKLKIGENIDV 1565
G++ G +K I + A + + G+L +S+ + K K LK G+ I V
Sbjct: 7 VGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILV 65
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 31.4 bits (72), Expect = 4.9
Identities = 27/140 (19%), Positives = 46/140 (32%), Gaps = 37/140 (26%)
Query: 390 IDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNK---KNYNTISKINNISKLQNN 446
I +F++I S + + N P S ++ + + N SK S+ +
Sbjct: 861 IRDFLRINLVKSPISYIRKR------NDPSSSGLLVQSNNFLDSTNIYSKAEIQSQSLS- 913
Query: 447 DMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNS--KRIIEIIT 504
Q Q ++ L R N E + ++ ILS+S RI
Sbjct: 914 --------QNQGTIRTLLNR--NKESQSLL---------------ILSSSDCFRIGPFNG 948
Query: 505 DELNIIKNKYGSHKKNIRRS 524
+ K + IR S
Sbjct: 949 KKSKYHNIKESNPLIPIRNS 968
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 30.8 bits (71), Expect = 5.9
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 12/51 (23%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVI 916
GP +GK T+A+++A + LSA+ + ++ +L VI
Sbjct: 43 GPPGTGKTTLARIIAGATDAPF---------EALSAVTSGVK---DLREVI 81
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and
metabolism].
Length = 216
Score = 30.4 bits (69), Expect = 6.0
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGF 885
VI I+G +GK T+AQ +A LGF
Sbjct: 5 MVIVIEGMIGAGKSTLAQALAEHLGF 30
>gnl|CDD|240199 cd05694, S1_Rrp5_repeat_hs2_sc2, S1_Rrp5_repeat_hs2_sc2: Rrp5 is a
trans-acting factor important for biogenesis of both the
40S and 60S eukaryotic ribosomal subunits. Rrp5 has two
distinct regions, an N-terminal region containing
tandemly repeated S1 RNA-binding domains (12 S1 repeats
in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in
Homo sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a specific
functional domain. Deletions within the S1-containing
region inhibit pre-rRNA processing at either site A3 or
A2, whereas deletions within the TPR region confer an
inability to support cleavage of A0-A2. This CD includes
H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat
2 (sc2). Rrp5 is found in eukaryotes but not in
prokaryotes or archaea.
Length = 74
Score = 28.4 bits (64), Expect = 6.0
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDLG--GIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
L EG + G V ++ D+G +D+G G G L D L +GQ + +
Sbjct: 2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAG------NFSKLKVGQLLLCVVE 55
Query: 1312 KYDQEKNRVSL 1322
K + VSL
Sbjct: 56 KVKDDGRVVSL 66
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.9 bits (68), Expect = 6.4
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDS 890
G +GK T+ + +A L ++D+
Sbjct: 9 GFMGAGKSTIGRALAKALNLPFIDT 33
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 30.3 bits (69), Expect = 6.6
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 853 TMIKKYIP-VITIDGPTASGKGTVAQLVASKLGFH 886
M K +I I G + SGK TVA+ ++ +LG
Sbjct: 1 MMKKPEKVIIIGIAGGSGSGKTTVAKELSEQLGVE 35
>gnl|CDD|130192 TIGR01122, ilvE_I, branched-chain amino acid aminotransferase,
group I. Among the class IV aminotransferases are two
phylogenetically separable groups of branched-chain
amino acid aminotransferase (IlvE). The last common
ancestor of the two lineages appears also to have given
rise to a family of D-amino acid aminotransferases
(DAAT). This model represents the IlvE family more
strongly similar to the DAAT family [Amino acid
biosynthesis, Pyruvate family].
Length = 298
Score = 30.4 bits (69), Expect = 6.9
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 219 TAGIIYGLSSVHDG---YYTGKGRVIIRAKTHIEEFNRENRTAIIID-ELPYQVNKKSLL 274
T + YG + V +G Y T KG I R K HI+ R +A I E+PY +K+ L+
Sbjct: 18 THALHYG-TGVFEGIRAYDTDKGPAIFRLKEHIQ---RLYDSAKIYRMEIPY--SKEELM 71
Query: 275 EKISQLVKEKKLE 287
E + +++ L
Sbjct: 72 EATRETLRKNNLR 84
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 30.1 bits (68), Expect = 6.9
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A ++A L ++ +G + R
Sbjct: 8 GPPGAGKGTQAVVLAEHLHIPHISTGDILR 37
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 30.6 bits (69), Expect = 6.9
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYL--DSGALYR 895
VI I GPT +GK +A +A +L + DS +YR
Sbjct: 23 VIVISGPTGAGKSRLALELAKRLNGEIISADSVQVYR 59
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 30.1 bits (68), Expect = 7.0
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A+ +A +LG L +G + R
Sbjct: 13 GPPGAGKGTQAERLAQELGLKKLSTGDILR 42
>gnl|CDD|213366 cd12832, TmCorA-like_u3, Uncharacterized subfamily of the
Thermotoga maritima CorA-like family. This subfamily
belongs to the Thermotoga maritima CorA (TmCorA)-like
family of the MIT superfamily of essential membrane
proteins involved in transporting divalent cations
(uptake or efflux) across membranes. Members of the
TmCorA-like family are found in all three kingdoms of
life. It is a functionally diverse family which includes
the CorA Co2+ transporter from the hyperthermophilic
Thermotoga maritima, and three Saccharomyces cerevisiae
proteins: two located in the plasma membrane: the Mg2+
transporter Alr1p/Swc3p and the putative Mg2+
transporter, Alr2p, and the vacuole membrane protein
Mnr2p, a putative Mg2+ transporter. Thermotoga maritima
CorA forms funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport by a related protein, Saccharomyces cerevisiae
Alr1p. Natural variants in this signature sequence may
be associated with the transport of different divalent
cations. The functional diversity of the MIT superfamily
may also be due to minor structural differences
regulating gating, substrate selection, and transport.
Length = 287
Score = 30.6 bits (70), Expect = 7.1
Identities = 19/115 (16%), Positives = 41/115 (35%), Gaps = 19/115 (16%)
Query: 437 INNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTD----- 491
I N+ + + M+K L K + YE ++K+ + D
Sbjct: 90 IANLKEKWLSGMHK----------CESPTELLLRIVKDALKTYEAPLEKLSEELDKYEEE 139
Query: 492 -ILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMV 545
L K + L +K K K+ + ++ +++ I+ + +QD+
Sbjct: 140 VFLKKRKGSLLK---RLYHLKRKASVIKRVLNLTQDVIDKIDTPLKSDPYTQDLR 191
>gnl|CDD|222186 pfam13509, S1_2, S1 domain. The S1 domain was originally identified
as a repeat motif in the ribosomal S1 protein. It was
later identified in a wide range of proteins. The S1
domain has an OB-fold structure. The S1 domain is
involved in nucleic acid binding.
Length = 61
Score = 27.5 bits (62), Expect = 7.7
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAII 1484
G+ + TDFG F LDG G + L P E+ + GDE+E +
Sbjct: 2 GKINTLKVLRETDFGYF--LDGGEGGEVLL-------PKREVPEELEIGDEVEVFL 48
>gnl|CDD|215747 pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.
Length = 320
Score = 30.3 bits (69), Expect = 7.8
Identities = 20/101 (19%), Positives = 32/101 (31%), Gaps = 8/101 (7%)
Query: 428 KKNYNTISKINNI--SKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYE--NVI 483
K I ++ + + Y LSD + + ++ T Y N I
Sbjct: 176 PKPSTATDTIRDLLEEPSLDENKYNLSD---KFVENHERRKPTTKAPGGGYPTYLLRNRI 232
Query: 484 KKVIDLTDILSNSKRIIEIITDELNI-IKNKYGSHKKNIRR 523
KV + ++ + I KN KNIRR
Sbjct: 233 DKVEEGKGPSFTYRKSGRGEAPKTGILGKNGERFRPKNIRR 273
>gnl|CDD|215203 PLN02355, PLN02355, probable galactinol--sucrose
galactosyltransferase 1.
Length = 758
Score = 30.6 bits (69), Expect = 7.9
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 214 APDFPTAGIIYGLSSVHDGYYTGKGRVIIRA 244
A +FP GII +S DG Y+ K +IRA
Sbjct: 425 ARNFPDNGIISCMSHNTDGLYSAKRTAVIRA 455
>gnl|CDD|145067 pfam01718, Orbi_NS1, Orbivirus non-structural protein NS1, or
hydrophobic tubular protein. This family consists of
orbivirus non-structural protein NS1, or hydrophobic
tubular protein. NS1 has no specific function in virus
replication, it is however thought to play a role in
transport of mature virus particles from virus inclusion
bodies to the cell membrane. Orbivirus are part of the
larger reoviridae which have a dsRNA genome of at least
10 segments encoding at least 10 viral proteins;
orbivirus found in this family include bluetongue virus,
and African horsesickness virus.
Length = 546
Score = 30.5 bits (69), Expect = 8.8
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 271 KSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIE-LKRNEIPEIV 316
KS +S+ + E+ E + L D SGMR ++ ++ P V
Sbjct: 87 KSADRPVSEDLAEEMQETLQALYDAYSHSGMREEVQGFRKRNDPARV 133
>gnl|CDD|222834 PHA01755, PHA01755, hypothetical protein.
Length = 562
Score = 30.3 bits (68), Expect = 9.5
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 6/64 (9%)
Query: 854 MIKKYIPVITIDGP--TASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAI-NNNIQLDN 910
+I K I G T SG +A L + YL + +R +TL + N+++Q++N
Sbjct: 126 LISKITIPNLIAGTQFTFSGSSNLASLTSQYFQSSYLQT---WRSITLQNLGNSSVQINN 182
Query: 911 ELEL 914
+ L
Sbjct: 183 SIYL 186
>gnl|CDD|238981 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
also known as uridine kinase or uridine-cytidine kinase
(UCK), catalyzes the reversible phosphoryl transfer from
ATP to uridine or cytidine to yield UMP or CMP. In the
primidine nucleotide-salvage pathway, this enzyme
combined with nucleoside diphosphate kinases further
phosphorylates UMP and CMP to form UTP and CTP. This
kinase also catalyzes the phosphorylation of several
cytotoxic ribonucleoside analogs such as 5-flurrouridine
and cyclopentenyl-cytidine.
Length = 198
Score = 29.8 bits (68), Expect = 9.6
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 861 VITIDGPTASGKGTVAQLVASKLG 884
+I I G + SGK TVA+ + +LG
Sbjct: 1 IIGIAGGSGSGKTTVAEEIIEQLG 24
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.137 0.384
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 83,602,686
Number of extensions: 8728150
Number of successful extensions: 9610
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9048
Number of HSP's successfully gapped: 405
Length of query: 1619
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1509
Effective length of database: 6,058,662
Effective search space: 9142520958
Effective search space used: 9142520958
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 66 (29.4 bits)