RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8969
(1230 letters)
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 898 bits (2322), Expect = 0.0
Identities = 355/695 (51%), Positives = 476/695 (68%), Gaps = 57/695 (8%)
Query: 133 ENDDNFNDHKVSL-------VKDLSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQE 185
E D V + E AL +E+ +T R++IS++ L++EQ +L
Sbjct: 95 ELSDKGGYLVVRVDNLKEEPFDKDDEEIKALTREIKETFRELISLSKLFREQPALLSA-- 152
Query: 186 NSPVVDNPIYLADLGAALTG-AEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKI 244
+D P LAD AA E E Q +LE ++I KRL +L LLKKELEL KLQ KI
Sbjct: 153 -LEDIDEPGRLADFVAASLQLKEKDELQEVLETVNIEKRLKKALELLKKELELLKLQNKI 211
Query: 245 GREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLN 304
++VEEK+++ R+Y L+EQLKAIKKELG+EKDDKD +E K +E++++ K+P V +V+
Sbjct: 212 TKKVEEKMEKTQREYYLREQLKAIKKELGIEKDDKDELE-KLKEKLEELKLPEEVKKVIE 270
Query: 305 EELAKLGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKK 364
+EL KL LE SSEF VTRNYLDWLT LPWG S+ENLDL +A +ILD+DHYG++ VK+
Sbjct: 271 KELTKLSLLEPSSSEFTVTRNYLDWLTDLPWGKYSKENLDLKRAKEILDEDHYGLKKVKE 330
Query: 365 RILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIK 424
RILE++AV +L+G +G ILC GPPGVGKTS+ KSIA+ALNR++ RFS+GG+ D AEI+
Sbjct: 331 RILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIR 390
Query: 425 GHRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANF 484
GHRRTYVGAMPG++IQ +KK KT+NPL L+DE+DKIG + GDPASALLE+LDPEQN F
Sbjct: 391 GHRRTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAF 450
Query: 485 LDHYLDVPVDLSRVLFICTANVIDTIPEPLRDRMEMIDVSGYVAEEKVAIAAQYLIPQAM 544
DHYLDVP DLS+V+FI TAN IDTIP PL DRME+I++SGY EEK+ IA +YLIP+A+
Sbjct: 451 SDHYLDVPFDLSKVIFIATANSIDTIPRPLLDRMEVIELSGYTEEEKLEIAKKYLIPKAL 510
Query: 545 KESGLSPEQITLEPSAIQVLIKNYCRESGVRNLQKHIEKVTRKVALTIVKKESDK----- 599
++ GL P+++ + A+ +LIK Y RE+GVRNL++ IEK+ RK A+ +V++ K
Sbjct: 511 EDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIEKICRKAAVKLVEQGEKKKSEAE 570
Query: 600 -VTVTNDNLSDFVGKPIFSHDRLFEITPPGVV----------------TRKVA----LTI 638
V +T DNL ++GKP+F+++R +E+TPPGVV T KVA L +
Sbjct: 571 SVVITPDNLKKYLGKPVFTYERAYEVTPPGVVMGLAWTPMGGDTLFIETTKVAGKGSLEL 630
Query: 639 ------VKKESDKV--TVTNDNLSDFVGKP-IFSHDRLFEITPPGVVMGLAWTAMAVKKD 689
V KES ++ T +D P F + P G A KD
Sbjct: 631 TGQLGDVMKESAQIALTYVRSIAADLGISPNFFEKADIHLHVPEG----------ATPKD 680
Query: 690 GPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILM 749
GPSAGIT+ TAL+SLATGKP++ ++AMTGEI+L GKVLP+GG+KEKTIAAKR G+ TI++
Sbjct: 681 GPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLPIGGLKEKTIAAKRAGIKTIIL 740
Query: 750 PEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVF 784
PE+N++D +LPE ++EGL +HFV + +V F
Sbjct: 741 PEKNRRDLEELPENVKEGLEIHFVKHYDEVLKKAF 775
Score = 189 bits (483), Expect = 1e-49
Identities = 75/133 (56%), Positives = 90/133 (67%), Gaps = 13/133 (9%)
Query: 939 GSTLFIETSVRKPTSVATDPADDKKSDGSLFLTGHLGDVMKESANISLTVARNFLSTIEP 998
G TLFIET+ GSL LTG LGDVMKESA I+LT R+ + +
Sbjct: 612 GDTLFIETTKVAG-------------KGSLELTGQLGDVMKESAQIALTYVRSIAADLGI 658
Query: 999 DNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVL 1058
F +HLHVPEGA KDGPSAGIT+ TAL+SLATGKP++ ++AMTGEI+L GKVL
Sbjct: 659 SPNFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVL 718
Query: 1059 PVGGIKEKTIALK 1071
P+GG+KEKTIA K
Sbjct: 719 PIGGLKEKTIAAK 731
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 827 bits (2140), Expect = 0.0
Identities = 305/674 (45%), Positives = 428/674 (63%), Gaps = 48/674 (7%)
Query: 147 KDLSEVYSALMQEVIKTVRDIISMNP-LYKEQLMILLQQENSPVVDNPIYLADLGAALTG 205
D AL++ ++ + +N + E+L L +D+P LAD AA
Sbjct: 122 IDEEREIEALVRSILSEFEEYAKLNKKIPPEELQSLNS------IDDPGKLADTIAAHLP 175
Query: 206 AEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQL 265
+ E+Q ILE +D+ +RL L LL+KE++L +L+++I ++V+E++++ R+Y L+EQL
Sbjct: 176 LKLEEKQEILETLDVKERLEKLLDLLEKEIDLLQLEKRIRKKVKEQMEKSQREYYLREQL 235
Query: 266 KAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRN 325
KAI+KELG + DDKD +EE RE+I+ K+P E +EL KL + S+E V RN
Sbjct: 236 KAIQKELGEDDDDKDEVEE-LREKIEKLKLPKEAKEKAEKELKKLETMSPMSAEATVIRN 294
Query: 326 YLDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILC 385
YLDWL LPWG +S++ LDL +A KILD DHYG+E VK+RILE++AV +L +G ILC
Sbjct: 295 YLDWLLDLPWGKRSKDKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILC 354
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKT 445
GPPGVGKTS+ KSIA+AL R++ R S+GG+ D AEI+GHRRTY+GAMPGK+IQ MKK
Sbjct: 355 LVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKA 414
Query: 446 KTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTAN 505
+NP+ L+DE+DK+G + GDPASALLE+LDPEQN F DHYL+VP DLS+V+FI TAN
Sbjct: 415 GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATAN 474
Query: 506 VIDTIPEPLRDRMEMIDVSGYVAEEKVAIAAQYLIPQAMKESGLSPEQITLEPSAIQVLI 565
+DTIP PL DRME+I +SGY +EK+ IA ++LIP+ +KE GL ++T+ AI+ +I
Sbjct: 475 SLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDII 534
Query: 566 KNYCRESGVRNLQKHIEKVTRKVALTIV-KKESDKVTVTNDNLSDFVGKPIFSHDRLFEI 624
+ Y RE+GVRNL++ I K+ RK A I+ KKE V + NL ++G P+F + + E
Sbjct: 535 RYYTREAGVRNLEREIAKICRKAAKKILLKKEKSIVKIDEKNLKKYLGVPVFRYGKAEEE 594
Query: 625 TPPGVVT--------------------RKVALTI------VKKESDKV--TVTNDNLSDF 656
GVVT K LT+ V KES + +
Sbjct: 595 DQVGVVTGLAWTEVGGDLLTIEAVKMPGKGKLTLTGSLGDVMKESAQAALSYVRSRAEKL 654
Query: 657 VGKPIFSHDRLFEI-TPPGVVMGLAWTAMAVKKDGPSAGITITTALVSLATGKPIKQNLA 715
P F R I P G A KDGPSAGIT+ TALVSL TGKP++ ++A
Sbjct: 655 GIDPDFFEKRDIHIHVPEG----------ATPKDGPSAGITMATALVSLLTGKPVRADVA 704
Query: 716 MTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILMPEENKKDFTDLPEYIREGLNVHFVSE 775
MTGEI+L G+VLP+GG+KEK +AA R G+ T+++P++N++D ++P+ ++EGL +H V
Sbjct: 705 MTGEITLRGRVLPIGGLKEKLLAAHRGGIKTVIIPKDNERDLEEIPDNVKEGLEIHPVKT 764
Query: 776 WRQVYDLVFEHTSE 789
+V L E
Sbjct: 765 IDEVLKLALVGNPE 778
Score = 176 bits (448), Expect = 3e-45
Identities = 66/131 (50%), Positives = 82/131 (62%), Gaps = 13/131 (9%)
Query: 939 GSTLFIETSVRKPTSVATDPADDKKSDGSLFLTGHLGDVMKESANISLTVARNFLSTIEP 998
G L IE G L LTG LGDVMKESA +L+ R+ +
Sbjct: 610 GDLLTIEAVK-------------MPGKGKLTLTGSLGDVMKESAQAALSYVRSRAEKLGI 656
Query: 999 DNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVL 1058
D F R +H+HVPEGA KDGPSAGIT+ TALVSL TGKP++ ++AMTGEI+L G+VL
Sbjct: 657 DPDFFEKRDIHIHVPEGATPKDGPSAGITMATALVSLLTGKPVRADVAMTGEITLRGRVL 716
Query: 1059 PVGGIKEKTIA 1069
P+GG+KEK +A
Sbjct: 717 PIGGLKEKLLA 727
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 483 bits (1244), Expect = e-155
Identities = 257/638 (40%), Positives = 384/638 (60%), Gaps = 62/638 (9%)
Query: 190 VDNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVE 249
+D+P LAD AA + ++Q++LE D+ +RL +++++ E++L +++++I V+
Sbjct: 159 IDDPARLADTIAAHMPLKLADKQSVLEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVK 218
Query: 250 EKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK 309
+++++ R+Y L EQ+KAI+KELG E DD E + +I K+P E EL K
Sbjct: 219 KQMEKSQREYYLNEQMKAIQKELG-EMDDAPDENEALKRKIDAAKMPKEAKEKAEAELQK 277
Query: 310 LGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILEF 369
L + S+E V R Y+DW+ +PW +S+ DL QA +ILD DHYG+E VK RILE+
Sbjct: 278 LKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLERVKDRILEY 337
Query: 370 IAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRT 429
+AV +G ILC GPPGVGKTS+ +SIA+A R+Y R ++GG+ D AEI+GHRRT
Sbjct: 338 LAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRT 397
Query: 430 YVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYL 489
Y+G+MPGK+IQ M K +NPL L+DE+DK+ GDPASALLE+LDPEQN F DHYL
Sbjct: 398 YIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYL 457
Query: 490 DVPVDLSRVLFICTANVIDTIPEPLRDRMEMIDVSGYVAEEKVAIAAQYLIPQAMKESGL 549
+V DLS V+F+ T+N ++ IP PL DRME+I +SGY +EK+ IA ++L+P+ ++ + L
Sbjct: 458 EVDYDLSDVMFVATSNSMN-IPAPLLDRMEVIRLSGYTEDEKLNIAKRHLLPKQIERNAL 516
Query: 550 SPEQITLEPSAIQVLIKNYCRESGVRNLQKHIEKVTRKVALTIVKKESDK-VTVTNDNLS 608
++T++ SAI +I+ Y RE+GVR+L++ I K+ RK ++ +S K + + DNL
Sbjct: 517 KKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDKSLKHIEINGDNLH 576
Query: 609 DFVGKPIFSHDRLFEITPPGVVTR------------------------------------ 632
D++G F + R G VT
Sbjct: 577 DYLGVQRFDYGRADNENRVGQVTGLAWTEVGGDLLTIETACVPGKGKLTYTGSLGEVMQE 636
Query: 633 --KVALTIVKKESDKVTVTNDNLSDFVGK-PIFSHDRLFEITPPGVVMGLAWTAMAVKKD 689
+ ALT+V+ ++K+ + DF K I H P G A KD
Sbjct: 637 SIQAALTVVRARAEKLGIN----PDFYEKRDIHVH------VPEG----------ATPKD 676
Query: 690 GPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILM 749
GPSAGI + TALVS TG P++ ++AMTGEI+L G+VLP+GG+KEK +AA R G+ T+L+
Sbjct: 677 GPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAAHRGGIKTVLI 736
Query: 750 PEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVFEHT 787
P ENK+D ++P+ + L++H V +V L ++
Sbjct: 737 PFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQNE 774
Score = 118 bits (298), Expect = 4e-27
Identities = 56/104 (53%), Positives = 73/104 (70%)
Query: 966 GSLFLTGHLGDVMKESANISLTVARNFLSTIEPDNTFLNTRHLHLHVPEGAVKKDGPSAG 1025
G L TG LG+VM+ES +LTV R + + F R +H+HVPEGA KDGPSAG
Sbjct: 622 GKLTYTGSLGEVMQESIQAALTVVRARAEKLGINPDFYEKRDIHVHVPEGATPKDGPSAG 681
Query: 1026 ITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIA 1069
I + TALVS TG P++ ++AMTGEI+L G+VLP+GG+KEK +A
Sbjct: 682 IAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLA 725
>gnl|CDD|191262 pfam05362, Lon_C, Lon protease (S16) C-terminal proteolytic domain.
The Lon serine proteases must hydrolyse ATP to degrade
protein substrates. In Escherichia coli, these proteases
are involved in turnover of intracellular proteins,
including abnormal proteins following heat-shock. The
active site for protease activity resides in a
C-terminal domain. The Lon proteases are classified as
family S16 in Merops.
Length = 205
Score = 168 bits (427), Expect = 2e-47
Identities = 77/214 (35%), Positives = 108/214 (50%), Gaps = 41/214 (19%)
Query: 601 TVTNDNLSDFVGKPIFSHDRLFEITPPGVVT----------------------RKVALT- 637
TVT NL ++G P F + + GVVT K+ LT
Sbjct: 1 TVTAKNLEKYLGVPRFRYGEAEKEDQVGVVTGLAWTEVGGDLLTIEATIMPGKGKLTLTG 60
Query: 638 ---IVKKESDKV--TVTNDNLSDFVGKPIFSHDRLFEITPPGVVMGLAWTAMAVKKDGPS 692
V KES + + + P F + I P A KDGPS
Sbjct: 61 QLGDVMKESAQAALSYVRSRAEELGIDPDFFEKKDIHIHVP---------EGATPKDGPS 111
Query: 693 AGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILMPEE 752
AG+T+ TALVS TG P+++++AMTGEI+L G+VLP+GG+KEK +AA R G+ T+++P+E
Sbjct: 112 AGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGGLKEKLLAAHRAGIKTVIIPKE 171
Query: 753 NKKDFTDLPEYIREGLNVHFVSEWRQVYDLVFEH 786
N+KD D+PE +REGL + V D V +H
Sbjct: 172 NEKDLEDIPENVREGLEIIPVEH----VDEVLKH 201
Score = 160 bits (407), Expect = 1e-44
Identities = 69/160 (43%), Positives = 95/160 (59%), Gaps = 25/160 (15%)
Query: 939 GSTLFIETSVRKPTSVATDPADDKKSDGSLFLTGHLGDVMKESANISLTVARNFLSTIEP 998
G L IE ++ G L LTG LGDVMKESA +L+ R+ +
Sbjct: 40 GDLLTIEATIMPGK-------------GKLTLTGQLGDVMKESAQAALSYVRSRAEELGI 86
Query: 999 DNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVL 1058
D F + +H+HVPEGA KDGPSAG+T+ TALVS TG P+++++AMTGEI+L G+VL
Sbjct: 87 DPDFFEKKDIHIHVPEGATPKDGPSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVL 146
Query: 1059 PVGGIKEKTIA-----LKPLIQQQEQHKSKMFIIVDLDDV 1093
P+GG+KEK +A +K +I +E K DL+D+
Sbjct: 147 PIGGLKEKLLAAHRAGIKTVIIPKENEK-------DLEDI 179
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 118 bits (298), Expect = 4e-31
Identities = 39/147 (26%), Positives = 59/147 (40%), Gaps = 30/147 (20%)
Query: 384 LCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMK 443
L YGPPG GKT++AK++A+ L + S + YVG ++ + +
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSEL---------VSKYVGESEKRLRELFE 51
Query: 444 KTKTENPLVL-IDEVDKIGK-------GYSGDPASALLEMLDPEQNANFLDHYLDVPVDL 495
K P V+ IDE+D + S + LL LD + L
Sbjct: 52 AAKKLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTS------------SL 99
Query: 496 SRVLFICTANVIDTIPEPL-RDRMEMI 521
S+V+ I N D + L R R + I
Sbjct: 100 SKVIVIAATNRPDKLDPALLRGRFDRI 126
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 94.5 bits (235), Expect = 1e-19
Identities = 48/96 (50%), Positives = 67/96 (69%), Gaps = 4/96 (4%)
Query: 689 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTIL 748
DGPSAG IT ++S GKPI+Q++A+TGEISL GK+ PVGGI EK AK+ G+ T++
Sbjct: 524 DGPSAGAAITLCMISAILGKPIRQDVAITGEISLRGKIKPVGGIFEKIYGAKQAGIKTVV 583
Query: 749 MPEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVF 784
+PEEN K D+P+ + G+ V FVS ++ +VF
Sbjct: 584 IPEENLK---DVPQGL-PGIEVKFVSTIEELMRIVF 615
Score = 71.4 bits (175), Expect = 2e-12
Identities = 48/130 (36%), Positives = 71/130 (54%), Gaps = 16/130 (12%)
Query: 937 FSGSTLFIETSVRKPTSVATDPADDKKSDGSLFLTGHLGDVMKESANISLTVARNFLSTI 996
F GS L IE +VA + + G++ G + K+S + +V R ++
Sbjct: 457 FVGSVLEIE-------AVAFEA--KEPGKGTVRFNDTAGSMAKDSVFNAASVIRK-ITGK 506
Query: 997 EPDNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGK 1056
+ N +H++V G + DGPSAG IT ++S GKPI+Q++A+TGEISL GK
Sbjct: 507 DLSNY-----DIHVNVIGGG-RIDGPSAGAAITLCMISAILGKPIRQDVAITGEISLRGK 560
Query: 1057 VLPVGGIKEK 1066
+ PVGGI EK
Sbjct: 561 IKPVGGIFEK 570
>gnl|CDD|223994 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational
modification, protein turnover, chaperones].
Length = 647
Score = 81.2 bits (201), Expect = 2e-15
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 689 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEK-------TIAAKR 741
DG SA + AL+S + P+ Q++A+TG I G+V PVGG+ EK AA
Sbjct: 513 DGDSASLAEACALISALSKIPVDQDIAITGSIDQFGEVQPVGGVNEKIEGFFRVCQAAGL 572
Query: 742 VGVHTILMPEENKKD 756
G +++P+ N KD
Sbjct: 573 TGEQGVIIPKANVKD 587
Score = 73.5 bits (181), Expect = 4e-13
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 1020 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEK 1066
DG SA + AL+S + P+ Q++A+TG I G+V PVGG+ EK
Sbjct: 513 DGDSASLAEACALISALSKIPVDQDIAITGSIDQFGEVQPVGGVNEK 559
Score = 30.0 bits (68), Expect = 9.3
Identities = 28/127 (22%), Positives = 47/127 (37%), Gaps = 20/127 (15%)
Query: 491 VPVDLSRVLFICTANVIDTIPEPLRDRMEMIDVSGYVA-------EEKVAIAAQYLIPQA 543
VP+DL +L ++ + EP R R+E + + Y+ Q
Sbjct: 273 VPLDLKLIL-AGNREDLEDLHEPDRSRIEGFGYEAEFEDTMPITDANRSKLVQFYV--QE 329
Query: 544 MKESGLSPEQITLEPSAIQVLIKNYCRESGVRN-----LQKHIEKVTRKVALTIVKKESD 598
+ G P L+ A++ LI+ R +G +N L+ V + A I E
Sbjct: 330 LARDGNIPH---LDKDAVEELIREAARRAGDQNKLTLRLRDLGNLV--REAGDIAVSEGR 384
Query: 599 KVTVTND 605
K+ D
Sbjct: 385 KLITAED 391
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 77.9 bits (192), Expect = 3e-15
Identities = 51/233 (21%), Positives = 87/233 (37%), Gaps = 44/233 (18%)
Query: 345 LTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARA 404
L + L+ G E+V + L + G + GPPGVGKT +A+++ARA
Sbjct: 15 LGKIRSELEKVVVGDEEVIELALLALLA--------GGHVLLEGPPGVGKTLLARALARA 66
Query: 405 LNREYFRFS----------VGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENPLVLI 454
L + R +G + A + +PG + + ++L+
Sbjct: 67 LGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFR--FVPGPLFAAV------RVILLL 118
Query: 455 DEVDKIGKGYSGDPA--SALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTANVID---- 508
DE+++ P +ALLE L+ Q + +P + I T N +
Sbjct: 119 DEINRA------PPEVQNALLEALEERQVTVPGLTTIRLP---PPFIVIATQNPGEYEGT 169
Query: 509 -TIPEPLRDRMEMIDVSGYV--AEEKVAIAAQYLIPQAMKESGLSPEQITLEP 558
+PE L DR + Y EE+ I A+ + L ++ E
Sbjct: 170 YPLPEALLDRFLLRIYVDYPDSEEEERIILARVGGVDELDLESLVKPVLSDEE 222
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 73.3 bits (180), Expect = 4e-15
Identities = 39/173 (22%), Positives = 63/173 (36%), Gaps = 35/173 (20%)
Query: 357 YGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRF---- 412
G E+ + + E + K L YGPPG GKT++A++IA L R F
Sbjct: 1 VGQEEAIEALREALE------LPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLN 54
Query: 413 --SVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPAS 470
+ VAE+ GH + K + ++ IDE+D + +G
Sbjct: 55 ASDLLEGLVVAELFGHFLVRLLF--------ELAEKAKPGVLFIDEIDSLSRG------- 99
Query: 471 ALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTANVID--TIPEPLRDRMEMI 521
L+ D+ +D V I N + L DR+++
Sbjct: 100 ------AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIR 146
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 79.4 bits (196), Expect = 5e-15
Identities = 33/65 (50%), Positives = 41/65 (63%)
Query: 689 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTIL 748
DGPSAG+ I A+ S PI +AMTGEISL G V PVGG+ K AAK+ G ++
Sbjct: 440 DGPSAGVAIAVAIYSAIFKCPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAKKAGAKKVI 499
Query: 749 MPEEN 753
+P EN
Sbjct: 500 IPYEN 504
Score = 65.6 bits (160), Expect = 8e-11
Identities = 38/93 (40%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 979 KESANISLTVARNFLSTIEPDNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLATG 1038
+ S L V R+ I P N +H++ P G + DGPSAG+ I A+ S
Sbjct: 406 RGSVENVLAVLRSVFG-INPQNY-----DIHINFP-GGIPVDGPSAGVAIAVAIYSAIFK 458
Query: 1039 KPIKQNLAMTGEISLVGKVLPVGGIKEKTIALK 1071
PI +AMTGEISL G V PVGG+ K A K
Sbjct: 459 CPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAK 491
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 77.3 bits (191), Expect = 3e-14
Identities = 28/68 (41%), Positives = 46/68 (67%)
Query: 689 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTIL 748
+G SA I++ TA++S P+ Q++AMTG +S+ G VLPVGG+ K AA G+ ++
Sbjct: 508 EGDSASISVATAVISALENIPVDQSVAMTGSLSVRGDVLPVGGVTYKIEAAAEAGIKKVI 567
Query: 749 MPEENKKD 756
+P+ N++D
Sbjct: 568 IPKSNEQD 575
Score = 66.6 bits (163), Expect = 5e-11
Identities = 46/147 (31%), Positives = 71/147 (48%), Gaps = 26/147 (17%)
Query: 963 KSDGSLFLTGHLGDVMKESA-NISLTVARNF---LSTIEPDNTFLNTRHLHLHVPEGAVK 1018
K +G + TG L ++ KE+ N+S + + +S + F+ T EG
Sbjct: 457 KEEGKVIATGKLKEIAKEAVQNVSAIIKKFTGKDISNYDIHIQFVQTY-------EGV-- 507
Query: 1019 KDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIALKPLIQQQE 1078
+G SA I++ TA++S P+ Q++AMTG +S+ G VLPVGG+ K I+
Sbjct: 508 -EGDSASISVATAVISALENIPVDQSVAMTGSLSVRGDVLPVGGVTYK-------IEAAA 559
Query: 1079 QHKSKMFII--VDLDDV---DREEDMI 1100
+ K II + DV D ED I
Sbjct: 560 EAGIKKVIIPKSNEQDVMIEDEYEDKI 586
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 76.8 bits (189), Expect = 4e-14
Identities = 33/97 (34%), Positives = 55/97 (56%), Gaps = 1/97 (1%)
Query: 689 DGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTIL 748
+G SA I++ TA++S P+ Q++AMTG +S+ G+VLPVGG+ EK AA G+ ++
Sbjct: 499 EGDSASISVATAVISALEEIPVDQDVAMTGSLSVRGEVLPVGGVTEKIEAAIEAGIKKVI 558
Query: 749 MPEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVFE 785
+P+ N D E + + V +V + V +
Sbjct: 559 IPKSNMIDVILEKET-EGKIEIIPVETLDEVLEHVLD 594
Score = 69.9 bits (171), Expect = 4e-12
Identities = 45/160 (28%), Positives = 75/160 (46%), Gaps = 18/160 (11%)
Query: 951 PTSVATDPADDKKSDGSLFLTGHLGDVMKESANISLTVARNFLSTIEPDNTFLNTRHLHL 1010
P PA+ K +G + TG LG++ KE+ + + + ++ +H+
Sbjct: 437 PIKAIVAPAE-SKEEGRIIATGKLGEIAKEAVTNVSALIKKYTGED------ISNYDIHI 489
Query: 1011 HVPEGAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAL 1070
+ +G SA I++ TA++S P+ Q++AMTG +S+ G+VLPVGG+ EK
Sbjct: 490 QFLQTYEGVEGDSASISVATAVISALEEIPVDQDVAMTGSLSVRGEVLPVGGVTEK---- 545
Query: 1071 KPLIQQQEQHKSKMFIIVDLDDVDREEDMIFELEDEDLME 1110
I+ + K II D+I E E E +E
Sbjct: 546 ---IEAAIEAGIKKVIIPK----SNMIDVILEKETEGKIE 578
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 69.1 bits (169), Expect = 7e-12
Identities = 50/268 (18%), Positives = 89/268 (33%), Gaps = 37/268 (13%)
Query: 354 DDHYGMEDVKKRILEFIAVS-------QLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
DD G+E+ K+ + E I + G K + YGPPG GKT +AK++A
Sbjct: 242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESR 301
Query: 407 REYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENPLVL-IDEVDKIGKGYS 465
+ + +VG + + +K + P ++ IDE+D + G
Sbjct: 302 SRFISVKGSELLS---------KWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRG 352
Query: 466 GDPASALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTANVIDTIPEPLRDRM---EMID 522
+ ++ LD VL I N D + L +I
Sbjct: 353 PSEDGSGRRVV---GQLLTE---LDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIY 406
Query: 523 VSGYVAEEKVAIAAQYLIPQAMKESGLSPEQITLEPSAIQVL--IKNYCRE---SGVRNL 577
V EE++ I +L + + + E + I RE +R
Sbjct: 407 VPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREA 466
Query: 578 ------QKHIEKVTRKVALTIVKKESDK 599
+K+ ++ +E +
Sbjct: 467 RRREVTLDDFLDALKKIKPSVTYEEWKE 494
>gnl|CDD|224664 COG1750, COG1750, Archaeal serine proteases [General function
prediction only].
Length = 579
Score = 65.2 bits (159), Expect = 1e-10
Identities = 45/151 (29%), Positives = 63/151 (41%), Gaps = 15/151 (9%)
Query: 654 SDFVGKPIFSHDRLFEITPPGVVMGLAWTAMAVKKDGPSAGITITTALVSLATGKPIKQN 713
G + S+D + V+G GPSAG +T A+ + G I+++
Sbjct: 89 LRLAGVDMSSYDVYIAVEADSPVVG-----------GPSAGGYMTVAIYAALMGWSIRKD 137
Query: 714 LAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILMPEENKKDFTDLPEYIRE-GLNVHF 772
+ MTG I+ G + PVGGI EK AA + G L+P + DL EY + GL V
Sbjct: 138 VMMTGMINPDGSIGPVGGILEKLEAAAKAGAKIFLIPVGQRI-VVDLVEYGKSLGLKVIE 196
Query: 773 VSEW-RQVYDLVFEHTSERPFPCPVLGCDRS 802
V Y L E P G + S
Sbjct: 197 VGTLEDAAYYLTG-PQIEPPETGVAEGQNYS 226
Score = 47.8 bits (114), Expect = 3e-05
Identities = 21/46 (45%), Positives = 30/46 (65%)
Query: 1021 GPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEK 1066
GPSAG +T A+ + G I++++ MTG I+ G + PVGGI EK
Sbjct: 114 GPSAGGYMTVAIYAALMGWSIRKDVMMTGMINPDGSIGPVGGILEK 159
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 60.8 bits (148), Expect = 1e-09
Identities = 46/216 (21%), Positives = 81/216 (37%), Gaps = 50/216 (23%)
Query: 360 EDVKKRILEFIAVSQLKGTTQGKI--LCFYGP-PGVGKTSIAKSIARALNREYFRFSVGG 416
K+ + +G+I + + P PG GKT++AK++ + E F G
Sbjct: 27 AADKETFKSIV--------KKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVL-FVNGS 77
Query: 417 MSDVAEIKGHRRTYVGAM----PGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASAL 472
+ ++ + + GKVI +IDE D++G + +
Sbjct: 78 DCRIDFVRNRLTRFASTVSLTGGGKVI-------------IIDEFDRLGLADAQRHLRSF 124
Query: 473 LEMLDPEQNANFLDHYLDVPVDLSRVLFICTANVIDTIPEPLRDRMEMIDVSGYVAEEKV 532
+E + N FI TAN + I EPLR R +ID EE++
Sbjct: 125 ME----AYSKN--------------CSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQI 166
Query: 533 AIAAQYLIPQAMKESGLSPEQITLEPSAIQVLIKNY 568
+ Q +I + L E + ++ + L+K
Sbjct: 167 EMMKQ-MIVRCKGI--LEAEGVEVDMKVLAALVKKN 199
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 57.0 bits (137), Expect = 3e-09
Identities = 31/148 (20%), Positives = 52/148 (35%), Gaps = 21/148 (14%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRR----TYVGAMP 435
G+++ GPPG GKT++A+++AR L D+ E +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 436 GKVIQCMKKT-----KTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLD 490
G ++ K + ++++DE+ + D L +L E L
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSL-----LDAEQEALLLLLEELRLLLLLKSEK 115
Query: 491 VPVDLSRVLFICTAN-VIDTIPEPLRDR 517
+ I T N D P LR R
Sbjct: 116 ------NLTVILTTNDEKDLGPALLRRR 137
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 59.7 bits (146), Expect = 5e-09
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 15/74 (20%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKT 445
+GPPG GKT++A+ IA A + + S S V +++ +VI+ ++
Sbjct: 41 LWGPPGTGKTTLARIIAGATDAPFEALS-AVTSGVKDLR------------EVIEEARQR 87
Query: 446 KT--ENPLVLIDEV 457
++ ++ IDE+
Sbjct: 88 RSAGRRTILFIDEI 101
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 53.3 bits (129), Expect = 5e-08
Identities = 39/131 (29%), Positives = 52/131 (39%), Gaps = 23/131 (17%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYV----GAMPGKV--- 438
F GP GVGKT +AK++A L + MS+ E V GA PG V
Sbjct: 8 FLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME-----EHSVSRLIGAPPGYVGYE 62
Query: 439 ---IQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLDVPVDL 495
+ +VLIDE++K G + LL++L+ D VD
Sbjct: 63 EGGQLTEAVRRKPYSIVLIDEIEKAHPGVQ----NDLLQILE---GGTLTDKQ-GRKVDF 114
Query: 496 SRVLFICTANV 506
LFI T N
Sbjct: 115 RNTLFIMTGNF 125
>gnl|CDD|216923 pfam02190, LON, ATP-dependent protease La (LON) domain. This
domain has been shown to be part of the PUA superfamily.
Length = 191
Score = 53.5 bits (129), Expect = 8e-08
Identities = 27/87 (31%), Positives = 53/87 (60%), Gaps = 7/87 (8%)
Query: 147 KDLSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLGAALTGA 206
++L E AL++E+I+ +++++ + L +LL+ ++ +++P LADL A+L
Sbjct: 112 EELLEALEALVKELIEKIKELLPLL----LPLELLLKIDD---IEDPGRLADLIASLLPL 164
Query: 207 EGTEQQAILEEMDIPKRLMLSLSLLKK 233
E+Q +LE +D+ +RL L LLK+
Sbjct: 165 SPEEKQELLETLDVKERLEKLLELLKR 191
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 55.1 bits (134), Expect = 1e-07
Identities = 22/101 (21%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 686 VKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVH 745
+K P+A + + A+ S +P+ + + GE+ L G++ PV I+ + A ++G
Sbjct: 352 LKITEPAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIERRLKEAAKLGFK 411
Query: 746 TILMPEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVFEH 786
++P+ N +G+ V V + +L+F
Sbjct: 412 RAIVPKGNLPKKPP------KGIEVIGVKTLAEALELLFGL 446
Score = 42.4 bits (101), Expect = 0.001
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 1015 GAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKE 1065
G +K P+A + + A+ S +P+ + + GE+ L G++ PV I+
Sbjct: 350 GGLKITEPAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIER 400
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 54.1 bits (131), Expect = 3e-07
Identities = 27/101 (26%), Positives = 50/101 (49%), Gaps = 8/101 (7%)
Query: 686 VKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVH 745
VK P+A + + ALVS +P+ Q+ + GE+ L G++ PV + + A ++G
Sbjct: 364 VKVTEPAADLAVALALVSSFRNRPLPQDTVVFGEVGLSGEIRPVPRGERRLKEAAKLGFK 423
Query: 746 TILMPEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLVFEH 786
++P+ N + EG+ V VS + ++VF+
Sbjct: 424 RAIVPKGNIP--------LPEGIKVIGVSTLAEALEVVFDI 456
Score = 45.3 bits (108), Expect = 2e-04
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 1015 GAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKE 1065
G VK P+A + + ALVS +P+ Q+ + GE+ L G++ PV +
Sbjct: 362 GGVKVTEPAADLAVALALVSSFRNRPLPQDTVVFGEVGLSGEIRPVPRGER 412
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 53.4 bits (129), Expect = 5e-07
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKT 445
+GPPG GKT++A+ IA N + S S V +++ ++I+ +K
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALS-AVTSGVKDLR------------EIIEEARKN 99
Query: 446 KTEN--PLVLIDEV 457
+ ++ +DE+
Sbjct: 100 RLLGRRTILFLDEI 113
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 52.6 bits (127), Expect = 8e-07
Identities = 57/225 (25%), Positives = 81/225 (36%), Gaps = 66/225 (29%)
Query: 358 GMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYF------- 410
G E K+++ E+I S LKG + K L YGPPGVGKTS+A ++A E
Sbjct: 18 GNEKAKEQLREWIE-SWLKGKPK-KALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQ 75
Query: 411 ------RFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKI-GKG 463
G + + G RR L+L+DEVD I G
Sbjct: 76 RTADVIERVAGEAATSGSLFGARRK---------------------LILLDEVDGIHGNE 114
Query: 464 YSGDPASALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTAN-VIDTIPEPLRDRMEMID 522
G A A+LE++ A P+ I TAN D LR+ MI+
Sbjct: 115 DRGG-ARAILELIK---KAK-------QPI-------ILTANDPYDPSLRELRNACLMIE 156
Query: 523 VSGYVAEEKVAIAAQYLIPQAMKESGLSPEQITLEPSAIQVLIKN 567
I +K E I + A++ + +
Sbjct: 157 FKRLSTRS---------IVPVLKRI-CRKEGIECDDEALKEIAER 191
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 48.8 bits (117), Expect = 1e-06
Identities = 34/147 (23%), Positives = 61/147 (41%), Gaps = 25/147 (17%)
Query: 384 LCFYGPPGVGKTSIAKSIARAL-NREYFRFSVGGMSDVAEIKGHRRTYVGAM---PGKVI 439
+ GPPG GK+ +A+ +A AL NR F + + ++KG R G G ++
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGPLV 61
Query: 440 QCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQ----NANFLDHYLDVPVDL 495
+ ++ + + ++DE+++ D ++LL +LD + L V
Sbjct: 62 RAAREGE----IAVLDEINRANP----DVLNSLLSLLDERRLLLPEGGEL-----VKAAP 108
Query: 496 SRVLFICTANVIDT----IPEPLRDRM 518
I T N +D + LR R
Sbjct: 109 DGFRLIATMNPLDRGLNELSPALRSRF 135
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction only].
Length = 467
Score = 51.6 bits (123), Expect = 2e-06
Identities = 22/78 (28%), Positives = 34/78 (43%)
Query: 1135 ENNVCPECKKTFSSAHHMKVHLRIHSGIRPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKP 1194
+ CP C +FS H+ H+R H+G +P +C C+K+FS H+RTH
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPS 91
Query: 1195 YRCAHEFCSKSFKTSGDL 1212
+ + K S
Sbjct: 92 DLNSKSLPLSNSKASSSS 109
Score = 46.6 bits (110), Expect = 6e-05
Identities = 45/195 (23%), Positives = 62/195 (31%), Gaps = 21/195 (10%)
Query: 790 RPFPCPVLGCDRSFTTSNIRKVHIRTHTGEKPYVCGEAGCDKSFASATNYKNHMRIHSGE 849
RP CP C SF+ HIR+HTGEKP C +GCDKSF+ H+R H
Sbjct: 32 RPDSCP--NCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNN 89
Query: 850 KPYVCQVRDCQKRFTEYSSLY--------------KHTLVHSDIRPFICDRCPRSYRQLC 895
+ SS H+L S P + D S +
Sbjct: 90 PSDLNSKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNN 149
Query: 896 TLNVHKKTNHRESKNKKPSNRVSNQLISIQSSLTSYYSFVHFSGSTLFIETSVRKPTSVA 955
L N+ S N SN + + S S + S+ + +
Sbjct: 150 PL----PGNNSSSVNTPQSNS-LHPPLPANSLSKDPSSNLSLLISSNVSTSIPSSSENSP 204
Query: 956 TDPADDKKSDGSLFL 970
+ S S
Sbjct: 205 LSSSYSIPSSSSDQN 219
Score = 45.8 bits (108), Expect = 1e-04
Identities = 28/125 (22%), Positives = 48/125 (38%), Gaps = 9/125 (7%)
Query: 826 EAGCDKSFASATNYKNHMR--IHSGE--KPYVCQVRDCQKRFTEYSSLYKHTLVHSDIRP 881
C+ SF+ ++ H+R HSGE KP+ C C K F+ +L +H L+H+ I P
Sbjct: 292 SKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351
Query: 882 FIC--DRCPRSYRQLCTLNVHKKTNHR--ESKNKKPSNRVSNQLISI-QSSLTSYYSFVH 936
+ L + +KK ++ + + + S S + H
Sbjct: 352 AKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITH 411
Query: 937 FSGST 941
S
Sbjct: 412 LSFRP 416
Score = 43.9 bits (103), Expect = 4e-04
Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 10/105 (9%)
Query: 1127 TVKKSTSSENNVCPECKKTFSSAHHMKVHLR--IHSG--IRPYKCPVEYCEKAFSTQYSR 1182
+ + S +C +FS + + HLR HSG ++P+ CP C K FS +
Sbjct: 280 SSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDAL 339
Query: 1183 KAHIRTHTGEKPYRCAHEFCSKSF------KTSGDLQKHVRTHTD 1221
K HI HT P + S F + LQ++ D
Sbjct: 340 KRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKND 384
Score = 43.1 bits (101), Expect = 7e-04
Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 1163 RPYKCPVEYCEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTSGDLQKHVRTHT 1220
RP CP C +FS HIR+HTGEKP +C++ C KSF +L +H+RTH
Sbjct: 32 RPDSCP--NCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
Score = 37.8 bits (87), Expect = 0.040
Identities = 20/87 (22%), Positives = 30/87 (34%), Gaps = 4/87 (4%)
Query: 790 RPFPCPVLGCDRSFTTSNIRKVHIRTHTGEKPYVCGEAGCDKSFASATNYKNHMRIHSGE 849
+ C R+F + +HI TH +PY C C KSF N H +IH+
Sbjct: 385 KKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNH 444
Query: 850 KPYVCQVRDCQKRFTEYSSLYKHTLVH 876
P +C + +
Sbjct: 445 APLLC----SILKSFRRDLDLSNHGKD 467
Score = 32.4 bits (73), Expect = 1.6
Identities = 33/131 (25%), Positives = 46/131 (35%), Gaps = 40/131 (30%)
Query: 1130 KSTSSENN---VCPE--CKKTFSSAHHMKVHLRIHSGIRPYKC----------------P 1168
+ S E+ CP C K FS +K H+ +H+ I P K P
Sbjct: 312 VNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEP 371
Query: 1169 VEY-------------------CEKAFSTQYSRKAHIRTHTGEKPYRCAHEFCSKSFKTS 1209
+ C + F + HI TH +PY C + CSKSF
Sbjct: 372 PQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRH 431
Query: 1210 GDLQKHVRTHT 1220
+L H + HT
Sbjct: 432 YNLIPHKKIHT 442
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 51.0 bits (123), Expect = 2e-06
Identities = 46/185 (24%), Positives = 71/185 (38%), Gaps = 52/185 (28%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFS 413
D+ G E VK+++ FI ++ +G +L +GPPG+GKT++A IA L + +
Sbjct: 26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVL-LFGPPGLGKTTLAHIIANELGVN-LKIT 83
Query: 414 VGGM----SDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPA 469
G D+A I G V+ IDE+ ++
Sbjct: 84 SGPALEKPGDLAAI------LTNLEEGDVL-------------FIDEIHRLSP------- 117
Query: 470 SALLEMLDP--EQNANFLDHYLD-----------VPVDLSRVLFICTANVIDTIPEPLRD 516
A+ E+L P E D LD + +DL I + PLRD
Sbjct: 118 -AVEEVLYPAME------DFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLRD 170
Query: 517 RMEMI 521
R +I
Sbjct: 171 RFGII 175
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 50.7 bits (122), Expect = 4e-06
Identities = 36/122 (29%), Positives = 61/122 (50%), Gaps = 20/122 (16%)
Query: 350 KILDDDHYGMEDVKKRILEFIAVSQLKGTTQ-----GKI---LCFYGPPGVGKTSIAKSI 401
K+ D G+++ K+ ++E V LK ++ KI + GPPG GKT +AK++
Sbjct: 51 KVTFKDVAGIDEAKEELMEI--VDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAV 108
Query: 402 ARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENP-LVLIDEVDKI 460
A + FS+ G SD E+ +VG +V ++ K P ++ IDE+D +
Sbjct: 109 AGEAGVPF--FSISG-SDFVEM------FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAV 159
Query: 461 GK 462
G+
Sbjct: 160 GR 161
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. All
proteins in this family for which functions are known
are 5'-3' DNA helicases that, as part of a complex with
RuvA homologs serve as a 5'-3' Holliday junction
helicase. RuvA specifically binds Holliday junctions as
a sandwich of two tetramers and maintains the
configuration of the junction. It forms a complex with
two hexameric rings of RuvB, the subunit that contains
helicase activity. The complex drives ATP-dependent
branch migration of the Holliday junction recombination
intermediate. The endonuclease RuvC resolves junctions
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 305
Score = 48.8 bits (117), Expect = 8e-06
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
+ G E VK+++ FI ++++ +L YGPPG+GKT++A IA +
Sbjct: 4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLL-LYGPPGLGKTTLAHIIANEMG 55
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 49.1 bits (118), Expect = 8e-06
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 10/60 (16%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKI--LCFYGPPGVGKTSIAKSIARALNREYFR 411
D+ G E++ +R+ ++ + + L F GPPG GKT+ A ++AR L E +R
Sbjct: 17 DEIVGQEEIVERLKSYVK--------EKNMPHLLFAGPPGTGKTTAALALARELYGEDWR 68
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 48.9 bits (116), Expect = 1e-05
Identities = 26/80 (32%), Positives = 32/80 (40%), Gaps = 24/80 (30%)
Query: 1161 GIRPYKCPVEYCEKAFSTQYSRKAHIRTH--------------------TGEKPYRCAHE 1200
+PYKCPVE C K + Q K H H +KPYRC E
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYH-MLHGHQNQKLHENPSPEKMNIFSAKDKPYRC--E 402
Query: 1201 FCSKSFKTSGDLQKHVRTHT 1220
C K +K L+ H R H+
Sbjct: 403 VCDKRYKNLNGLKYH-RKHS 421
Score = 42.4 bits (99), Expect = 0.001
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 818 GEKPYVCGEAGCDKSFASATNYKNHMRIHSGEKPYVCQVRDCQKRFTEYSSLYKHTLVHS 877
KPY C GC+K + + K HM +H ++ E S K + +
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHM-LHG----------HQNQKLHENPSPEKMNIFSA 394
Query: 878 DIRPFICDRCPRSYRQLCTLNVHKKTNH 905
+P+ C+ C + Y+ L L H+K +H
Sbjct: 395 KDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
Score = 42.0 bits (98), Expect = 0.002
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 13/84 (15%)
Query: 789 ERPFPCPVLGCDRSFTTSNIRKVHIRTHTGEKPYVCGEAGCDKSFASATNYKNHMRIHSG 848
+P+ CPV GC++ + N K H+ ++ + + +
Sbjct: 347 GKPYKCPVEGCNKKYKNQNGLKYHML-----------HGHQNQKLHENPSPEKMNIFSAK 395
Query: 849 EKPYVCQVRDCQKRFTEYSSLYKH 872
+KPY C+V C KR+ + L H
Sbjct: 396 DKPYRCEV--CDKRYKNLNGLKYH 417
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 42.4 bits (100), Expect = 2e-05
Identities = 15/28 (53%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 1181 SRKAHIRTHTGEKPYRCAHEFCSKSFKT 1208
+ + H+RTHTGEKPY+C C KSF +
Sbjct: 1 NLRRHMRTHTGEKPYKC--PVCGKSFSS 26
Score = 41.6 bits (98), Expect = 3e-05
Identities = 14/28 (50%), Positives = 22/28 (78%), Gaps = 2/28 (7%)
Query: 1151 HMKVHLRIHSGIRPYKCPVEYCEKAFST 1178
+++ H+R H+G +PYKCPV C K+FS+
Sbjct: 1 NLRRHMRTHTGEKPYKCPV--CGKSFSS 26
Score = 40.8 bits (96), Expect = 6e-05
Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 838 NYKNHMRIHSGEKPYVCQVRDCQKRFT 864
N + HMR H+GEKPY C V C K F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPV--CGKSFS 25
Score = 40.5 bits (95), Expect = 7e-05
Identities = 16/26 (61%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 810 KVHIRTHTGEKPYVCGEAGCDKSFAS 835
+ H+RTHTGEKPY C C KSF+S
Sbjct: 3 RRHMRTHTGEKPYKCPV--CGKSFSS 26
Score = 30.4 bits (69), Expect = 0.24
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 786 HTSERPFPCPVLGCDRSFTT 805
HT E+P+ CPV C +SF++
Sbjct: 9 HTGEKPYKCPV--CGKSFSS 26
Score = 28.1 bits (63), Expect = 1.7
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 868 SLYKHTLVHSDIRPFICDRCPRSYRQ 893
+L +H H+ +P+ C C +S+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|226011 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
[Signal transduction mechanisms].
Length = 342
Score = 48.2 bits (115), Expect = 2e-05
Identities = 40/166 (24%), Positives = 61/166 (36%), Gaps = 46/166 (27%)
Query: 594 KKESDKVTVTNDNLSDFVGKPIFSHDRLFEITPPGVVTRKVALTIVKKESDKVTVTNDNL 653
KK D+VT+ + P +VT + I ++ K
Sbjct: 174 KKPGDEVTIDYER----------------HNETPEIVTITL---IKNDDNGKA------- 207
Query: 654 SDFVGKPIFSHDRLFEITPPGVVMGLAWTAMAVKKDGPSAGITITTALVS------LATG 707
+G + + PP V GPSAG+ + A+ L G
Sbjct: 208 --GIGISLVDAPEV--WAPPDVDFNTE------NIGGPSAGLMFSLAIYDQLTKGDLTGG 257
Query: 708 KPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTILMPEEN 753
+ I A TG I + GKV P+GGI +K +AA + G +P +N
Sbjct: 258 RFI----AGTGTIEVDGKVGPIGGIDQKVVAAAKAGADVFFVPADN 299
Score = 37.4 bits (87), Expect = 0.044
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 10/56 (17%)
Query: 1020 DGPSAGITITTALVS------LATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIA 1069
GPSAG+ + A+ L G+ I A TG I + GKV P+GGI +K +A
Sbjct: 233 GGPSAGLMFSLAIYDQLTKGDLTGGRFI----AGTGTIEVDGKVGPIGGIDQKVVA 284
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 48.3 bits (115), Expect = 2e-05
Identities = 50/213 (23%), Positives = 85/213 (39%), Gaps = 34/213 (15%)
Query: 316 HSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKR---ILEFIAV 372
S + + ++ P E D+T DD G E+ K++ I+E++
Sbjct: 89 VPSGGGIITSTTIFVLETPREEDREIISDITL------DDVIGQEEAKRKCRLIMEYLEN 142
Query: 373 SQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVG 432
+ G K + FYGPPG GKT +AK++A + E+ G +VG
Sbjct: 143 PERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLL------LVKATELIGE---HVG 193
Query: 433 AMPGKVIQCMKKTKTENP-LVLIDEVDKIG--KGYS---GDPASALLEMLDPEQNANFLD 486
++ + ++ + P +V IDE+D I + Y GD + + N L
Sbjct: 194 DGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIV----------NALL 243
Query: 487 HYLDVPVDLSRVLFICTANVIDTIPEPLRDRME 519
LD + V+ I N + + +R R E
Sbjct: 244 TELDGIKENEGVVTIAATNRPELLDPAIRSRFE 276
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 48.5 bits (116), Expect = 2e-05
Identities = 41/121 (33%), Positives = 58/121 (47%), Gaps = 20/121 (16%)
Query: 351 ILDDDHYGMEDVKKRILEFIAVSQLK--------GTTQGKILCFYGPPGVGKTSIAKSIA 402
I D G+E+ K+ E VS LK G K + GPPG GKT +AK+IA
Sbjct: 180 ITFRDIAGIEEAKEEFEEV--VSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIA 237
Query: 403 RALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENP-LVLIDEVDKIG 461
+ FS+ G S+ E+ +VG +V KK K +P +V IDE+D +G
Sbjct: 238 GEAEVPF--FSISG-SEFVEM------FVGVGAARVRDLFKKAKENSPCIVFIDEIDAVG 288
Query: 462 K 462
+
Sbjct: 289 R 289
>gnl|CDD|205719 pfam13541, ChlI, Subunit ChlI of Mg-chelatase.
Length = 121
Score = 44.7 bits (107), Expect = 2e-05
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 686 VKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVH 745
+KK+G S + I +++ P + GE+SL G + PV G +AA+++G
Sbjct: 54 LKKEGSSFDLPIAIGILAAQGQIPALNDTVFLGELSLDGSLRPVRGALPIALAARKLGFK 113
Query: 746 TILMPEEN 753
+++P+EN
Sbjct: 114 GLIVPKEN 121
Score = 31.2 bits (72), Expect = 1.0
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 1017 VKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIALKPLIQQ 1076
+KK+G S + I +++ P + GE+SL G + PV G +A +
Sbjct: 54 LKKEGSSFDLPIAIGILAAQGQIPALNDTVFLGELSLDGSLRPVRGALPIALAAR----- 108
Query: 1077 QEQHKSKMFII 1087
+ K I+
Sbjct: 109 --KLGFKGLIV 117
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 47.7 bits (114), Expect = 4e-05
Identities = 59/238 (24%), Positives = 96/238 (40%), Gaps = 60/238 (25%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKV------- 438
F GP GVGKT +AK +A L RF MS+ E K +G+ PG V
Sbjct: 488 FVGPTGVGKTELAKQLAEELGVHLLRFD---MSEYME-KHTVSRLIGSPPGYVGFEQGGL 543
Query: 439 ----IQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLDVPVD 494
++ K + ++L+DE++K D + LL+++D A D+ D
Sbjct: 544 LTDAVR-----KHPHCVLLLDEIEKAHP----DIYNILLQVMD---YATLTDNNGRK-AD 590
Query: 495 LSRVLFICTANV------------------------IDTI--PEPLRDRMEMIDVSGYVA 528
V+ I T+N I + PE R+R++ I ++
Sbjct: 591 FRNVILIMTSNAGASEMSKPPIGFGGENSESKSLKAIKKLFSPE-FRNRLDAIIHFNDLS 649
Query: 529 EEKVAIAAQYLIPQAMKESGLSPEQITLEPS--AIQVLI-KNYCRESGVRNLQKHIEK 583
EE + + + + L+ + I LE + A + L K Y E G R L + I++
Sbjct: 650 EEMAEKIVKKFLDEL--QDQLNEKNIELELTDDAKKYLAEKGYDEEFGARPLARVIQE 705
Score = 34.2 bits (79), Expect = 0.57
Identities = 32/137 (23%), Positives = 53/137 (38%), Gaps = 41/137 (29%)
Query: 344 DLTQ-AAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILC--------FYGPPGVGK 394
DLT+ A D G ED +R ++ +LC G PGVGK
Sbjct: 170 DLTEKAKNGKIDPLIGREDELERTIQ--------------VLCRRKKNNPLLVGEPGVGK 215
Query: 395 TSIAKSIARAL----------NREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKK 444
T+I + +A + N + + +G + +A K Y G ++ + +
Sbjct: 216 TAIVEGLALRIAEGKVPERLKNAKIYSLDMGTL--LAGTK-----YRGDFEERLKAVVSE 268
Query: 445 -TKTENPLVLIDEVDKI 460
K N ++ IDE+ I
Sbjct: 269 IEKEPNAILFIDEIHTI 285
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 46.3 bits (111), Expect = 6e-05
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
D+ G E VK+ + FI ++ +G +L YGPPG+GKT++A IA +
Sbjct: 25 DEFIGQEKVKENLKIFIEAAKKRGEALDHVL-LYGPPGLGKTTLANIIANEMG 76
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 44.2 bits (105), Expect = 2e-04
Identities = 45/256 (17%), Positives = 82/256 (32%), Gaps = 53/256 (20%)
Query: 157 MQEVIKTVRDIISMNPLYKEQL----MILLQQENSPVVDNPIYLADLGAALTGAEGTEQQ 212
M+E + V+ E+L +IL ++ V +T A E+
Sbjct: 11 MREALAKVK----------EELGPDAVILSTRK----VRKGGLFGKKFVEVTAAIDEEEV 56
Query: 213 AILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 272
A + K+ + K L+ E Q + +L E ++KEL
Sbjct: 57 AAASAEEEAKKALEPADPAKLPATAEPLELPAPLEEPAAPAAQAAEPLLPE--AELRKEL 114
Query: 273 GLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWLTS 332
++ +E ++ P L E L + G E + E
Sbjct: 115 ---SALRELLERLLAGLALQRR--DPEGAKLLERLLEAGVSEELARE------------- 156
Query: 333 LPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGT--TQGKILCFYGPP 390
L + D +++ + + V + +G ++ GP
Sbjct: 157 ------------LLEKLPEDLDAEDAWRWLREALEGMLPVKPEEDPILERGGVIALVGPT 204
Query: 391 GVGK-TSIAKSIARAL 405
GVGK T++AK AR +
Sbjct: 205 GVGKTTTLAKLAARFV 220
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger is
the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be
any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those that
are important for the stable fold of the zinc finger. The
final position can be either his or cys. The C2H2 zinc
finger is composed of two short beta strands followed by
an alpha helix. The amino terminal part of the helix
binds the major groove in DNA binding zinc fingers. The
accepted consensus binding sequence for Sp1 is usually
defined by the asymmetric hexanucleotide core GGGCGG but
this sequence does not include, among others, the GAG
(=CTC) repeat that constitutes a high-affinity site for
Sp1 binding to the wt1 promoter.
Length = 22
Score = 37.7 bits (88), Expect = 7e-04
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 1138 VCPECKKTFSSAHHMKVHLRIH 1159
CP+C K+FS ++K HLR H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 33.5 bits (77), Expect = 0.020
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 1196 RCAHEFCSKSFKTSGDLQKHVRTH 1219
+C C KSF +L++H+RTH
Sbjct: 1 KC--PDCGKSFSRKSNLKRHLRTH 22
Score = 32.3 bits (74), Expect = 0.048
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 829 CDKSFASATNYKNHMRIH 846
C KSF+ +N K H+R H
Sbjct: 5 CGKSFSRKSNLKRHLRTH 22
Score = 31.9 bits (73), Expect = 0.064
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 1166 KCPVEYCEKAFSTQYSRKAHIRTH 1189
KCP C K+FS + + K H+RTH
Sbjct: 1 KCP--DCGKSFSRKSNLKRHLRTH 22
Score = 27.7 bits (62), Expect = 2.6
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 853 VCQVRDCQKRFTEYSSLYKHTLVH 876
C DC K F+ S+L +H H
Sbjct: 1 KCP--DCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus.
The RuvB protein makes up part of the RuvABC revolvasome
which catalyzes the resolution of Holliday junctions
that arise during genetic recombination and DNA repair.
Branch migration is catalyzed by the RuvB protein that
is targeted to the Holliday junction by the structure
specific RuvA protein. This family contains the
N-terminal region of the protein.
Length = 231
Score = 42.0 bits (100), Expect = 8e-04
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
D++ G E VK+ + FI ++ +G +L YGPPG+GKT++A IA +
Sbjct: 24 DEYIGQEKVKENLKIFIEAAKKRGEALDHVL-LYGPPGLGKTTLANIIANEMG 75
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 43.4 bits (103), Expect = 8e-04
Identities = 73/304 (24%), Positives = 118/304 (38%), Gaps = 72/304 (23%)
Query: 222 KRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDA 281
RL + ELE Q +I +E E+ + + K ++ E +K KE + + +K+
Sbjct: 393 VRLEIDKPEELDELERELAQLEIEKEALEREQDEKEKKLIDEIIK--LKEGRIPELEKEL 450
Query: 282 IEEKFRERIKD---KKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWLTSLPWGIQ 338
E + I + + PV ++L +E KL LE + + Q
Sbjct: 451 EAEVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRLKKRVI--------------GQ 496
Query: 339 SEENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIA 398
E ++ A + G+ D + I F+ F GP GVGKT +A
Sbjct: 497 DEAVEAVSDAIRR---ARAGLGDPNRPIGSFL---------------FLGPTGVGKTELA 538
Query: 399 KSIARALN---REYFRFSVGGMSD------VAEIKGHRRTYVGAMPGKVIQCMKKTKTE- 448
K++A AL + R MS+ V+ + G YVG G + TE
Sbjct: 539 KALAEALFGDEQALIRI---DMSEYMEKHSVSRLIGAPPGYVGYEEGGQL-------TEA 588
Query: 449 ---NP--LVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFL-DHYLDVPVDLSRVLFIC 502
P ++L+DE++K D + LL++LD L D VD + I
Sbjct: 589 VRRKPYSVILLDEIEKAHP----DVFNLLLQVLD----DGRLTDGQGRT-VDFRNTIIIM 639
Query: 503 TANV 506
T+N
Sbjct: 640 TSNA 643
Score = 34.6 bits (80), Expect = 0.36
Identities = 59/309 (19%), Positives = 106/309 (34%), Gaps = 94/309 (30%)
Query: 210 EQQAILEEMDIPKRLMLSLSLLKKELE--LNKLQQKIGR------------EVEEKVKQQ 255
+ +L I L L++ELE ++KL + +G +
Sbjct: 39 KGDELLNLCGID------LDKLRQELEEFIDKLPKVLGSPYLSPRLKRVLERAWLLAQSL 92
Query: 256 HRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLES 315
+Y+ E L L L + + ++ +K V E++ E G E
Sbjct: 93 GDEYVSTEHLL-----LALLNEPESVAAYILKKLGVTRK---DVEELIEE---LRGGNEV 141
Query: 316 HSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAAKILDDDH-YGMEDVKKRILEFIAVSQ 374
S ++ L+ + DLT+ A+ D G ++ +R ++
Sbjct: 142 DSKNAEEDQDALE-----------KYTRDLTELAREGKLDPVIGRDEEIRRTIQ------ 184
Query: 375 LKGTTQGKILC--------FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGH 426
IL G PGVGKT+I + +A+ + DV E
Sbjct: 185 --------ILSRRTKNNPVLVGEPGVGKTAIVEGLAQRIVNG----------DVPESLKD 226
Query: 427 RRTYVGAMP---------GKVIQCMKK-----TKTENPLVLIDEVDKI-----GKGYSGD 467
+R Y + G+ + +K K++N ++ IDE+ I +G + D
Sbjct: 227 KRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMD 286
Query: 468 PASALLEML 476
A+ L L
Sbjct: 287 AANLLKPAL 295
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 42.0 bits (99), Expect = 9e-04
Identities = 44/232 (18%), Positives = 82/232 (35%), Gaps = 41/232 (17%)
Query: 249 EEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELA 308
K R L L+ +K E +A+ E + K+ E L L
Sbjct: 1 MMMNKLIER---LHSLLQRLKLESI-----AEALPELLEQAADCKEWGY--AEFLEYLLE 50
Query: 309 KLGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILE 368
+ + + R S P + D + K+ LE
Sbjct: 51 EE--KLAREARKIERRLRSA---SFPAK------------KTFEEFDFEFQPGIDKKALE 93
Query: 369 FIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFR---FSVGGMSDVAEIKG 425
+A S ++ +G+ L GPPGVGKT +A +I L + + + ++++K
Sbjct: 94 DLA-SLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL--LSKLKA 150
Query: 426 HRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLD 477
G + K+++ +KK L++ID++ A L +++
Sbjct: 151 AFDE--GRLEEKLLRELKKV----DLLIIDDIGYEPFSQEE--ADLLFQLIS 194
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 43.0 bits (102), Expect = 0.001
Identities = 44/205 (21%), Positives = 74/205 (36%), Gaps = 22/205 (10%)
Query: 213 AILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 272
A+ E+ K +L K + LQ + EK + Q + E
Sbjct: 50 AVDEDETPKKNPVLREEKRKPAKSILSLQALL-----EKRPSRTNSQDALLQAENALPEW 104
Query: 273 GLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKL-GFLESHSSEFNVTRNYLDWLT 331
E + +E+ + + KV ++ L +EL +L LE S
Sbjct: 105 KKELEKPSEPKEEEPKAAAESKVVQKELDELRDELKELKNLLEDQLSGLRQVERIPPEFA 164
Query: 332 SLPWGIQSEENLDLTQ--AAKILDD--DHYG--MEDVKKRILEFIAVSQLKGTT-----Q 380
L + + L+ A K+L +H + +LE +A + + Q
Sbjct: 165 EL---YKRLKRSGLSPEIAEKLLKLLLEHMPPRERTAWRYLLELLA-NMIPVRVEDILKQ 220
Query: 381 GKILCFYGPPGVGK-TSIAKSIARA 404
G ++ GP GVGK T++AK AR
Sbjct: 221 GGVVALVGPTGVGKTTTLAKLAARY 245
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 37.1 bits (86), Expect = 0.001
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 1138 VCPECKKTFSSAHHMKVHLRIH 1159
CPEC K F S ++ H+R H
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
Score = 35.9 bits (83), Expect = 0.003
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 1195 YRCAHEFCSKSFKTSGDLQKHVRTH 1219
YRC C K FK+ L++H+RTH
Sbjct: 1 YRC--PECGKVFKSKSALREHMRTH 23
Score = 32.4 bits (74), Expect = 0.047
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 822 YVCGEAGCDKSFASATNYKNHMRIH 846
Y C E C K F S + + HMR H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 31.3 bits (71), Expect = 0.14
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 1165 YKCPVEYCEKAFSTQYSRKAHIRTH 1189
Y+CP C K F ++ + + H+RTH
Sbjct: 1 YRCP--ECGKVFKSKSALREHMRTH 23
Score = 29.0 bits (65), Expect = 0.77
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 852 YVCQVRDCQKRFTEYSSLYKHTLVH 876
Y C C K F S+L +H H
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 42.7 bits (100), Expect = 0.001
Identities = 34/115 (29%), Positives = 54/115 (46%), Gaps = 16/115 (13%)
Query: 355 DHYGMEDVKKRILEFIAVSQLKGTTQ---GKI---LCFYGPPGVGKTSIAKSIARALNRE 408
D G ++ K+ + E + + Q GKI + GPPG GKT +AK+IA
Sbjct: 153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVP 212
Query: 409 YFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENP-LVLIDEVDKIGK 462
+F S SD E+ +VG +V ++ K P ++ IDE+D +G+
Sbjct: 213 FFTIS---GSDFVEM------FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGR 258
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 42.4 bits (100), Expect = 0.001
Identities = 54/170 (31%), Positives = 75/170 (44%), Gaps = 26/170 (15%)
Query: 387 YGPPGVGKTSIAKSIARAL-NREYFRFSVGGMSDVAEIKGHR--RTYVGAMPG--KVI-- 439
YGPPG GKT IAK++A +L R GG S IKG YVG ++I
Sbjct: 222 YGPPGCGKTLIAKAVANSLAARIG--AEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQ 279
Query: 440 QCMKKTKTENP-LVLIDEVDKI----GKGYSGDPASALLEMLDPEQNANFLDHYLDVPVD 494
+ +K P +V DE+D + G G S D + ++ L E +D
Sbjct: 280 RAREKASEGRPVIVFFDEMDSLFRTRGSGVSSDVETTVVPQLLAE---------IDGVES 330
Query: 495 LSRVLFICTANVIDTI-PEPLR-DRMEM-IDVSGYVAEEKVAIAAQYLIP 541
L V+ I +N D I P LR R+++ I + AE I A+YL
Sbjct: 331 LDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKYLTD 380
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 42.1 bits (99), Expect = 0.001
Identities = 71/291 (24%), Positives = 116/291 (39%), Gaps = 62/291 (21%)
Query: 301 EVLNEELAKLGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDL-----TQAAKILD-- 353
++L EEL ES E +YL P + + +LD QA K+L
Sbjct: 41 DILEEELGTR--KESKEYEEEFELSYL------PTPKEIKAHLDEYVIGQEQAKKVLSVA 92
Query: 354 -DDHYGMEDVKKRILEFIAVSQLKGTTQGK--ILCFYGPPGVGKTSIAKSIARALNREYF 410
+HY KR+ G K IL GP G GKT +A+++AR LN
Sbjct: 93 VYNHY------KRLNFEKNKKSDNGVELSKSNIL-LIGPTGSGKTLLAQTLARILN---V 142
Query: 411 RFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKT------KTENPLVLIDEVDKIGK-- 462
F++ + + E YVG ++ + + K + ++ IDE+DKI +
Sbjct: 143 PFAIADATTLTEAG-----YVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKS 197
Query: 463 -------GYSGDPA-SALLEMLD------PEQNANFLDHYLDVPVDLSRVLFICTANVID 508
SG+ ALL++++ P Q + + +D S +LFIC
Sbjct: 198 ENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSNILFIC-GGAFV 256
Query: 509 TIPEPLRDRMEMIDVSGYVAEEKVAIAAQ-----YLIPQAMKESGLSPEQI 554
+ + ++ R G+ AE K + + P+ + + GL PE I
Sbjct: 257 GLEKIIKKRTGK-SSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFI 306
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 41.9 bits (99), Expect = 0.001
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 350 KILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREY 409
+ D D +GME+ +R + + + + +IL GP G GK+S+ + + R L EY
Sbjct: 47 RFFDHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL-EEY 105
Query: 410 FRFSVG 415
+ G
Sbjct: 106 SKTDEG 111
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 41.8 bits (99), Expect = 0.002
Identities = 14/21 (66%), Positives = 16/21 (76%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKTSIA+ A+ALN
Sbjct: 41 FSGPRGTGKTSIARIFAKALN 61
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 42.1 bits (99), Expect = 0.002
Identities = 20/69 (28%), Positives = 38/69 (55%)
Query: 686 VKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVH 745
VK P+A + + A+VS +P+ +L GE+ L G++ PV ++E+ A ++G
Sbjct: 366 VKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEERLKEAAKLGFK 425
Query: 746 TILMPEENK 754
++P+ N
Sbjct: 426 RAIVPKANS 434
Score = 40.2 bits (94), Expect = 0.007
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 1015 GAVKKDGPSAGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEK 1066
G VK P+A + + A+VS +P+ +L GE+ L G++ PV ++E+
Sbjct: 364 GGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEER 415
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 38.8 bits (91), Expect = 0.002
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 384 LCFYGPPGVGKTSIAKSIARALNREY 409
+ YGPPG GK+++AK +ARAL +
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHL 26
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 41.7 bits (98), Expect = 0.002
Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 10/75 (13%)
Query: 387 YGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTK 446
YGPPG GKT +AK++A + R VG S+ + Y+G P V + +
Sbjct: 185 YGPPGTGKTMLAKAVAHHTTATFIRV-VG--SEFVQ------KYLGEGPRMVRDVFRLAR 235
Query: 447 TENP-LVLIDEVDKI 460
P ++ IDEVD I
Sbjct: 236 ENAPSIIFIDEVDSI 250
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 38.8 bits (90), Expect = 0.003
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 383 ILCFYGPPGVGKTSIAKSIARALNREYF 410
I+ GPPG GK+++AK +A L
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVI 28
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to pfam05362, which is
the Lon protease C-terminal proteolytic domain, from
MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST] [Hypothetical proteins, Conserved].
Length = 675
Score = 41.4 bits (97), Expect = 0.003
Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 2/88 (2%)
Query: 690 GPS--AGITITTALVSLATGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRVGVHTI 747
GPS A + AL S +P+++ + + G +++ G + PV + A G +
Sbjct: 576 GPSTEASLAALIALCSALLKRPVQEQMVILGSMTIGGVINPVQDLAGSLQLAMDSGAKRV 635
Query: 748 LMPEENKKDFTDLPEYIREGLNVHFVSE 775
L+P + +D +P + + F S+
Sbjct: 636 LIPMSSARDIPTVPAELFSKFQISFYSD 663
Score = 33.3 bits (76), Expect = 0.98
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 1/83 (1%)
Query: 978 MKESANISLTVARNFLSTIEPDNTFLNTRHLHLHVPEGAVKKDGPSAGITITTALVSLAT 1037
KES ++ + L I F + HLHV + A + AL S
Sbjct: 536 AKESIRVAFDYFKGNLVRISASAKF-SEHDYHLHVVDLHNTGPSTEASLAALIALCSALL 594
Query: 1038 GKPIKQNLAMTGEISLVGKVLPV 1060
+P+++ + + G +++ G + PV
Sbjct: 595 KRPVQEQMVILGSMTIGGVINPV 617
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 41.2 bits (97), Expect = 0.004
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 20/79 (25%)
Query: 384 LCFYGPPGVGKTSIAKSIARALNREYFRFS--VGGMSDV-AEIK--GHRRTYVGAMPGKV 438
L YGPPGVGKT++A+ IA + + + G+ D+ AE+ R G
Sbjct: 55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGVKDLRAEVDRAKERLERHG------ 108
Query: 439 IQCMKKTKTENPLVLIDEV 457
K+T ++ IDEV
Sbjct: 109 ----KRT-----ILFIDEV 118
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains a
number of divergent C2H2 type zinc fingers.
Length = 24
Score = 34.9 bits (80), Expect = 0.006
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 1195 YRCAHEFCSKSFKTSGDLQKHVRTH 1219
++C C KSF + L++H+R H
Sbjct: 1 FKC--PLCGKSFSSKDALKRHLRKH 23
Score = 34.5 bits (79), Expect = 0.010
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 1138 VCPECKKTFSSAHHMKVHLRIH 1159
CP C K+FSS +K HLR H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKH 23
Score = 33.0 bits (75), Expect = 0.035
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 1165 YKCPVEYCEKAFSTQYSRKAHIRTH 1189
+KCP C K+FS++ + K H+R H
Sbjct: 1 FKCP--LCGKSFSSKDALKRHLRKH 23
Score = 29.9 bits (67), Expect = 0.38
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 822 YVCGEAGCDKSFASATNYKNHMRIH 846
+ C C KSF+S K H+R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
Score = 28.4 bits (63), Expect = 1.3
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 792 FPCPVLGCDRSFTTSNIRKVHIRTH 816
F CP+ C +SF++ + K H+R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 37.6 bits (88), Expect = 0.008
Identities = 18/87 (20%), Positives = 32/87 (36%), Gaps = 14/87 (16%)
Query: 383 ILCFYGPPGVGKTSIAKSIARAL-NREYFRFSVGGMSDVAEI----------KGHRRTYV 431
I G G GKT++ + +AR L NR + ++ T
Sbjct: 6 IGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTA 65
Query: 432 GAMPGKVIQCMKKTKTENPLVLIDEVD 458
+ ++ +K+ PL++IDE
Sbjct: 66 -ELLEAILDALKRRGR--PLLIIDEAQ 89
>gnl|CDD|197740 smart00464, LON, Found in ATP-dependent protease La (LON).
N-terminal domain of the ATP-dependent protease La
(LON), present also in other bacterial ORFs.
Length = 92
Score = 36.3 bits (84), Expect = 0.011
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 180 ILLQQENSPVVDNPIYLADLGAALTGAEGTEQQAILEEMDIPKRLMLSLSL 230
LLQ + + + P L+D AAL E E+Q +LE KRL + L
Sbjct: 45 FLLQDDPT---ETPEPLSDTIAALMPLELHEKQELLELEGTNKRLEKVIKL 92
>gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 358
Score = 39.0 bits (91), Expect = 0.011
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARAL 405
D +GME+ +RI+ + + + +IL GP G GK+S+A+ + + L
Sbjct: 58 ADFFGMEETIERIVNYFRHAAQGLEERKQILYLLGPVGGGKSSLAERLKKLL 109
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 39.4 bits (92), Expect = 0.012
Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 14/84 (16%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVI 439
+G IL YGPPG GKT +AK++A + + R VG S++ + Y+G P K++
Sbjct: 218 KGVIL--YGPPGTGKTLLAKAVANETSATFLRV-VG--SELIQ------KYLGDGP-KLV 265
Query: 440 QCMKKTKTEN--PLVLIDEVDKIG 461
+ + + EN +V IDE+D IG
Sbjct: 266 RELFRVAEENAPSIVFIDEIDAIG 289
>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 = 37.5 bits (88), Expect = 0.013
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGMS 418
GP G GK+++AK +A+ L Y GG+
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPY--LDTGGIR 34
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 38.9 bits (91), Expect = 0.014
Identities = 54/220 (24%), Positives = 83/220 (37%), Gaps = 39/220 (17%)
Query: 213 AILEEMDIPKRLMLSLSLLKKELELNKL------QQKIGREVEEKVKQQHRKYI------ 260
IL I K L L K +E+ KL +K KVK + +
Sbjct: 27 VILSNRRIKKGGFLGLLFSKTAVEVTKLAAVDSELRKFQTREAAKVKDAEAQLLKDPAEK 86
Query: 261 LQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEF 320
+E+ KA KK E+ IE K +E K + E++ +E + LE EF
Sbjct: 87 KREERKAAKKI---ERSTPSLIERKTQE---VKDSGEEIAEMMRDEKVPIRELEEIPPEF 140
Query: 321 NVTRNYLDWLTSLPWGIQSEENLDLTQA-------AKILDDDHYGMEDV----KKRILEF 369
IQS L+L +ILD ED+ +K
Sbjct: 141 VALYKQ---------EIQSPTRLNLINELLRAGLELEILDMKDESYEDLRYFSEKLRKLL 191
Query: 370 IAVSQLKGTTQGKILCFYGPPGVGK-TSIAKSIARALNRE 408
+++ + Q +++ GP GVGK T++AK AR + +
Sbjct: 192 LSLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLK 231
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 39.4 bits (92), Expect = 0.014
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 10/80 (12%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKV------I 439
F GP GVGKT + +++AL E RF MS+ E R +GA PG V +
Sbjct: 493 FAGPTGVGKTEVTVQLSKALGIELLRFD---MSEYMERHTVSR-LIGAPPGYVGFDQGGL 548
Query: 440 QCMKKTKTENPLVLIDEVDK 459
K + ++L+DE++K
Sbjct: 549 LTDAVIKHPHAVLLLDEIEK 568
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 38.7 bits (90), Expect = 0.021
Identities = 34/123 (27%), Positives = 58/123 (47%), Gaps = 17/123 (13%)
Query: 346 TQAAKILDDDHYGMEDVKKRILEFIAVS-------QLKGTTQGKILCFYGPPGVGKTSIA 398
+ K+ +D G+++ K++I E + + + G K + YGPPG GKT +A
Sbjct: 170 RKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLA 229
Query: 399 KSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENP-LVLIDEV 457
K++A YF S+ G EI Y G ++ + K+ + P ++ IDE+
Sbjct: 230 KAVANEAG-AYF-ISING----PEIMS---KYYGESEERLREIFKEAEENAPSIIFIDEI 280
Query: 458 DKI 460
D I
Sbjct: 281 DAI 283
Score = 38.3 bits (89), Expect = 0.031
Identities = 40/171 (23%), Positives = 74/171 (43%), Gaps = 23/171 (13%)
Query: 354 DDHYGMEDVKKRILEFI-------AVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
D G+E+VK+ + E + + + G K + +GPPG GKT +AK++A
Sbjct: 453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG 512
Query: 407 REYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKTENP-LVLIDEVDKIGKGYS 465
+ +V G +++ +VG + + +K + P ++ DE+D I
Sbjct: 513 ANF--IAVRGPEILSK-------WVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARG 563
Query: 466 GDPASALLEMLDPEQNANFLDHYLDVPVDLSRVLFICTANVIDTI-PEPLR 515
+++ + + N L +D +LS V+ I N D + P LR
Sbjct: 564 ARFDTSVTDRI-----VNQLLTEMDGIQELSNVVVIAATNRPDILDPALLR 609
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 38.2 bits (89), Expect = 0.022
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 10/76 (13%)
Query: 387 YGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTK 446
YGPPG GKT +AK++A N + R V G V R Y+G V + + K
Sbjct: 162 YGPPGTGKTLLAKAVAHETNATFIR--VVGSELV-------RKYIGEGARLVREIFELAK 212
Query: 447 TENP-LVLIDEVDKIG 461
+ P ++ IDE+D I
Sbjct: 213 EKAPSIIFIDEIDAIA 228
>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 = 36.8 bits (86), Expect = 0.023
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 388 GPPGVGKTSIAKSIARALNREYF 410
G G GKT++ + +A+AL +
Sbjct: 6 GMMGAGKTTVGRLLAKALGLPFV 28
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 36.9 bits (86), Expect = 0.023
Identities = 28/119 (23%), Positives = 50/119 (42%), Gaps = 19/119 (15%)
Query: 363 KKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSD-VA 421
++ I E + + Q + L GPPGVGKT +A ++ R + D V
Sbjct: 32 RRLIAELAGLDWI---EQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTPDLVE 88
Query: 422 EIKGHRRTYVGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGY---SGDPASALLEMLD 477
++K R G + + + K L+++D++ GY S + A L E++
Sbjct: 89 QLKRARGD--GRLARTLQRLAKA-----DLLILDDI-----GYLPLSQEAAHLLFELIS 135
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 37.1 bits (87), Expect = 0.025
Identities = 13/37 (35%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 378 TTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSV 414
++G ++ GP GVGK+++ K++ L + RFSV
Sbjct: 1 MSKGLLIVLSGPSGVGKSTLVKAL---LEDDKLRFSV 34
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 36.8 bits (86), Expect = 0.029
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 12/44 (27%)
Query: 388 GPPGVGKTSIAKSIARALNREYF--------RFSVGGMSDVAEI 423
G G GK++I +++A+ALN + R GMS +AEI
Sbjct: 9 GFMGAGKSTIGRALAKALNLPFIDTDQEIEKRT---GMS-IAEI 48
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 37.6 bits (88), Expect = 0.030
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 359 MEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARAL 405
ME + ++ FI + L FYG G GKT ++ IA+ L
Sbjct: 165 MEKILEKCKNFIENF----DKNNENLLFYGNTGTGKTFLSNCIAKEL 207
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 36.4 bits (85), Expect = 0.038
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGM 417
GPPGVGKT++ K + L E VGG
Sbjct: 6 GPPGVGKTTLVKKVIELLKSE--GVKVGGF 33
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 36.0 bits (83), Expect = 0.042
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 357 YGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFS 413
G E+ +R+L+ + G + GP G GKTS+ + + L +
Sbjct: 3 VGREEELERLLDALR-RARSGGPP--SVLLTGPSGTGKTSLLRELLEGLLVAAGKCD 56
>gnl|CDD|185352 PRK15455, PRK15455, PrkA family serine protein kinase; Provisional.
Length = 644
Score = 37.7 bits (88), Expect = 0.046
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 10/50 (20%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQG-----KILCFYGPPGVGKTSIA 398
++ YGME+ ++I VS + QG +IL GP G GK+S+A
Sbjct: 76 EEFYGMEEAIEQI-----VSYFRHAAQGLEEKKQILYLLGPVGGGKSSLA 120
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 37.4 bits (87), Expect = 0.048
Identities = 14/21 (66%), Positives = 18/21 (85%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP GVGKT+IA+ +A+ALN
Sbjct: 43 FSGPRGVGKTTIARILAKALN 63
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 35.2 bits (82), Expect = 0.052
Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 15/84 (17%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNRE---YFRFSVGGMSDVAEIKGHRRTYVGAMPG 436
KI+ GP VGKT++ + L E Y D +
Sbjct: 1 NNKIIVITGPRQVGKTTLLLQFLKELLSENILYINL------DDPRFLRLALLDL----- 49
Query: 437 KVIQCMKKTKTENPLVLIDEVDKI 460
+ + +K + +DE+ K+
Sbjct: 50 -LEEFLKLLLPGKKYLFLDEIQKV 72
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 35.9 bits (84), Expect = 0.056
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 388 GPPGVGKTSIAKSIARALNREYF 410
G G GK++I + +A+ L ++
Sbjct: 11 GFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 37.4 bits (87), Expect = 0.056
Identities = 51/249 (20%), Positives = 102/249 (40%), Gaps = 39/249 (15%)
Query: 137 NFNDHKVSLVKDLSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYL 196
F + +V DL +YS ++ + ++ + L E+ +++ ++ ++ +YL
Sbjct: 37 GFQGEDIEIV-DLPGIYSL----TTFSLEEEVARDYLLNEKPDLVVNVVDASNLERNLYL 91
Query: 197 ADLGAALTGAEGTEQQAILEEMDIPKRLMLSL-SLLKKE---LELNKLQQKIGREVEEKV 252
T Q L E+ IP L L+L +K+ ++ KL++++G V
Sbjct: 92 ------------TLQ---LLELGIPMILALNLVDEAEKKGIRIDEEKLEERLGVPVVPTS 136
Query: 253 KQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK--- 309
++ AI+K +GL++ K AIE E + +V ++E++ +
Sbjct: 137 AT--EGRGIERLKDAIRKAIGLKELKKRAIEI-VPEAYQVVEVVEGLIEIIYSISKRGLE 193
Query: 310 --LGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAA---KILDDDHYGMEDVKK 364
LG LE S E L + S NL T+ A ++L + G + + +
Sbjct: 194 ILLGLLEDLSLEIEKIERNLAEVVIKE----SPSNLSPTEIADEDRVLVEKSIGRKILDR 249
Query: 365 RILEFIAVS 373
+ I +
Sbjct: 250 FLGLPIFLF 258
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 37.3 bits (87), Expect = 0.057
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 10/77 (12%)
Query: 387 YGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTK 446
GPPG GKT +AK++A F G SD E+ +VG +V ++ K
Sbjct: 189 VGPPGTGKTLLAKAVAGEAGV-PFFSISG--SDFVEM------FVGVGASRVRDLFEQAK 239
Query: 447 TENP-LVLIDEVDKIGK 462
P ++ IDE+D +G+
Sbjct: 240 KNAPCIIFIDEIDAVGR 256
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 35.7 bits (83), Expect = 0.062
Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGM--SDVAEIKGHR 427
GPPGVGKT++ IA L E ++ VGG +V E G R
Sbjct: 7 GPPGVGKTTLVLKIAELLKEEGYK--VGGFYTEEVRE-GGKR 45
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 36.8 bits (86), Expect = 0.070
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKTS AK A+A+N
Sbjct: 43 FSGPRGTGKTSAAKIFAKAVN 63
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 36.2 bits (84), Expect = 0.076
Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 15/113 (13%)
Query: 386 FYGPPGVGKTSIAKSIA-RALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKK 444
GP G GK+++ K +A R L R GG V + KG A+ G+VI
Sbjct: 6 IVGPSGSGKSTLLKLLALRLLAR-------GGRVIVIDPKGEYSGLARALGGEVIDLGPG 58
Query: 445 TKTE-NPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLDVPVDLS 496
+ NPL I + + D + L++L L+ + DL+
Sbjct: 59 SGISLNPL-DIFPTGEDAEELEADAHARKLDLL-----LALLELAALLGRDLT 105
>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 = 34.9 bits (81), Expect = 0.078
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 388 GPPGVGKTSIAKSIARALNREYFR 411
G G GK+++ K++A L +
Sbjct: 6 GVSGSGKSTVGKALAERLGAPFID 29
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 34.8 bits (81), Expect = 0.078
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 388 GPPGVGKTSIAKSIARALNREYFR 411
G PG+ KT +A+++AR+L ++ R
Sbjct: 6 GVPGLAKTLLARTLARSLGLDFRR 29
>gnl|CDD|200217 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 36.0 bits (83), Expect = 0.095
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 352 LDDDHYGMEDVKKRILEFIA---VSQLK------GTTQGKILCFYGPPGVGKTSIAKSIA 402
LD + G++ VK RI E A V + + + F G PG GKT++A +A
Sbjct: 20 LDRELIGLKPVKTRIREIAALLLVERARQKLGLASAAPTLHMSFTGNPGTGKTTVALRMA 79
Query: 403 RALNR 407
+ L+R
Sbjct: 80 QILHR 84
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 35.3 bits (82), Expect = 0.12
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 379 TQGKILCFYGPPGVGKTSIAKS 400
T+ + YGPPG+GKTS+AK+
Sbjct: 1 TKNIKVLIYGPPGIGKTSLAKT 22
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 353
Score = 35.8 bits (83), Expect = 0.12
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 360 EDVKKRILEFIAVSQLK-GTTQGKILCFYGPPGVGKTSIAKSIA 402
++++KR F A+ + +G+ +C GP G GKT++ + IA
Sbjct: 8 DNIRKRFGAFTALKDISLSVKKGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
Length = 287
Score = 35.5 bits (82), Expect = 0.13
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 340 EENLDLTQAAKILDD---DHYGMEDVKKRILEFIA---VSQLK------GTTQGKILCFY 387
+E + TQ ++LD + G+ VK RI E A + +L+ + G + F
Sbjct: 6 QEEYEKTQIQEVLDILDEELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFT 65
Query: 388 GPPGVGKTSIAKSIARALNR 407
G PG GKT++A +A L +
Sbjct: 66 GSPGTGKTTVALKMADILYK 85
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 34.5 bits (80), Expect = 0.15
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 390 PGVGKTSIAKSIARALNREYF 410
G GK++I + +A+AL +
Sbjct: 1 MGAGKSTIGRLLAKALGLPFI 21
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 35.9 bits (83), Expect = 0.15
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 368 EFIAVSQLKGTTQGKI---LCFYGPPGVGKTSIAKSIARALN 406
+F+ + KI F GP GVGKTS A++ AR LN
Sbjct: 22 DFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLN 63
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 35.6 bits (82), Expect = 0.16
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 347 QAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
+A I D+ G E VK+ +L + +L G F GP GVGKT+ A+ IA A+N
Sbjct: 7 RARPITFDEVVGQEHVKEVLLAALRQGRL-----GHAYLFSGPRGVGKTTTARLIAMAVN 61
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 34.9 bits (81), Expect = 0.17
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHR-RTYVG 432
+G+ + GP G GK+++ K + L V G+ +E R VG
Sbjct: 29 KGERVLLIGPNGSGKSTLLKLLNGLLKPTSGEVLVDGLDTSSEKSLLELRQKVG 82
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 35.3 bits (82), Expect = 0.18
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 10/76 (13%)
Query: 387 YGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTK 446
YGPPG GKT +AK++A + + R V G V + Y+G V + + +
Sbjct: 191 YGPPGTGKTLLAKAVANQTDATFIR--VVGSELV-------QKYIGEGARLVRELFELAR 241
Query: 447 TENP-LVLIDEVDKIG 461
+ P ++ IDE+D IG
Sbjct: 242 EKAPSIIFIDEIDAIG 257
>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 = 34.5 bits (80), Expect = 0.18
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 383 ILCFYGPPGVGKTSIAKSIARALN 406
+ GPPG GK + A+ +A+
Sbjct: 1 RILLLGPPGSGKGTQAERLAKKYG 24
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 35.6 bits (82), Expect = 0.19
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 21/63 (33%)
Query: 358 GMEDVKKRILEFIAVSQLKGTTQGKI---------------LCFYGPPGVGKTSIAKSIA 402
G+E VK+ V+ LK +T + + F GPPG GKT+IA+ +A
Sbjct: 280 GLERVKR------QVAALKSSTAMALARAERGLPVAQTSNHMLFAGPPGTGKTTIARVVA 333
Query: 403 RAL 405
+
Sbjct: 334 KIY 336
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 35.1 bits (81), Expect = 0.19
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 9/55 (16%)
Query: 358 GMEDVKKRILE---FIAVSQ------LKGTTQGKILCFYGPPGVGKTSIAKSIAR 403
G+++VK I E +I +++ LK + Q + F G PG GKT++A+ + +
Sbjct: 10 GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK 64
>gnl|CDD|224050 COG1125, OpuBA, ABC-type proline/glycine betaine transport systems,
ATPase components [Amino acid transport and metabolism].
Length = 309
Score = 35.0 bits (81), Expect = 0.21
Identities = 40/147 (27%), Positives = 62/147 (42%), Gaps = 24/147 (16%)
Query: 360 EDVKKRILEFIAVSQLKGTTQ-GKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGG-- 416
E+V KR AV + T + G+ L GP G GKT+ K I R + + G
Sbjct: 5 ENVSKRYGNKKAVDDVNLTIEEGEFLVLIGPSGSGKTTTLKMINRLIEPTSGEILIDGED 64
Query: 417 MSDVAEIKGHRRT-YV----GAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASA 471
+SD+ ++ R+ YV G P + EN + + ++ K A
Sbjct: 65 ISDLDPVELRRKIGYVIQQIGLFPHLTVA-------EN-IATVPKLLGWDKERIKKRADE 116
Query: 472 LLEM--LDPEQNANFLDHYLDVPVDLS 496
LL++ LDP + + D Y P +LS
Sbjct: 117 LLDLVGLDPSE---YADRY---PHELS 137
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 33.8 bits (78), Expect = 0.21
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 381 GKILCFYGPPGVGKTSIAKSIARAL 405
G + G PG GK+++A +A A+
Sbjct: 33 GGLTLLAGAPGTGKSTLALDLAAAV 57
>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 = 33.9 bits (78), Expect = 0.21
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 388 GPPGVGKTSIAKSIARALNREY 409
GPPG GKT++AK +A L+ +
Sbjct: 7 GPPGSGKTTVAKILAEKLSLKL 28
>gnl|CDD|225357 COG2766, PrkA, Putative Ser protein kinase [Signal transduction
mechanisms].
Length = 649
Score = 35.1 bits (81), Expect = 0.24
Identities = 16/55 (29%), Positives = 31/55 (56%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
+D +GME+ ++I+ + + + +IL GP G GK+S+A+ + R + R
Sbjct: 76 NDFFGMEESIEQIVGYFKHAAQGLEERKQILYLLGPVGGGKSSLAERLKRLMERV 130
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.3 bits (82), Expect = 0.24
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 13/99 (13%)
Query: 686 VKKDGPSAGITITTALVSLATGKPIKQNLAMT---GEISLVGKVLPVGGIKEKTIAAKRV 742
+ K+G + I ++ A+G+ L + GE+SL G + PVGG+ +AAK
Sbjct: 60 LPKEGSRFDLPIALGIL-AASGQLPADALILYEFLGELSLDGLLRPVGGVLPAALAAKEK 118
Query: 743 GVHTILMPEENKKDFTDLPE--YIREGLNVHFVSEWRQV 779
G +++P+EN E I GL V+ +V
Sbjct: 119 GKRGLIVPKEN------AEEASLI-GGLPVYGARYLEEV 150
Score = 30.3 bits (69), Expect = 7.0
Identities = 24/59 (40%), Positives = 26/59 (44%), Gaps = 21/59 (35%)
Query: 361 DVK-----KRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAK---------SIARAL 405
DVK KR LE IA + G G L GPPG GKT +A SI AL
Sbjct: 180 DVKGQEQAKRALE-IAAA---G---GHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEAL 231
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 35.1 bits (81), Expect = 0.26
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 386 FYGPPGVGKTSIAKSIARALNRE 408
F G GVGKTS A+ +A+ALN E
Sbjct: 43 FTGARGVGKTSTARILAKALNCE 65
>gnl|CDD|191111 pfam04849, HAP1_N, HAP1 N-terminal conserved region. This family
represents an N-terminal conserved region found in
several huntingtin-associated protein 1 (HAP1)
homologues. HAP1 binds to huntingtin in a polyglutamine
repeat-length-dependent manner. However, its possible
role in the pathogenesis of Huntington's disease is
unclear. This family also includes a similar N-terminal
conserved region from hypothetical protein products of
ALS2CR3 genes found in the human juvenile amyotrophic
lateral sclerosis critical region 2q33-2q34.
Length = 307
Score = 34.8 bits (80), Expect = 0.26
Identities = 28/113 (24%), Positives = 54/113 (47%), Gaps = 11/113 (9%)
Query: 206 AEGTEQQAILE---EMDIPKRLMLSLS--LLKKELELNKLQQKIGREVEEKVKQQHRKYI 260
E EQQ + + ++ + SLS L KK +L + Q++I + + V Q +
Sbjct: 194 YEEKEQQLVNDCVKQLREANDQIASLSEELAKKTEDLERQQEEITHLLSQIVDLQKKCKS 253
Query: 261 LQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNE---ELAKL 310
+ + +++ L KD + ++ + +E ++DK ME+L+E EL L
Sbjct: 254 YALENEELQQHLAAAKDAQRQLQAELQE-LQDK--YAECMEMLHEAQEELKNL 303
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 34.6 bits (80), Expect = 0.27
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 384 LCFYGPPGVGKTSIAKSIARAL 405
+ FYGP GKT++A++IA A+
Sbjct: 116 VWFYGPASTGKTNLAQAIAHAV 137
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 35.3 bits (81), Expect = 0.28
Identities = 28/181 (15%), Positives = 69/181 (38%), Gaps = 4/181 (2%)
Query: 142 KVSLVKDLSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLGA 201
K+ + +++ +K + +EQL LQ++ + + + L +
Sbjct: 326 KLEKELKKEKEEIEELEKELKELEIKREAEEEEEEQLE-KLQEKLEQLEEELLAKKKLES 384
Query: 202 ALTGAEGTEQQAILEEMDIPKRLMLSLSLL--KKELELNKLQQKIGREVEEKVK-QQHRK 258
+ ++ LE + ++ L L ++E L + +++ + VEE + + ++
Sbjct: 385 ERLSSAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQ 444
Query: 259 YILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSS 318
L E+ + ++K+ DK +++ + K V L KL S
Sbjct: 445 GKLTEEKEELEKQALKLLKDKLELKKSEDLLKETKLVKLLEQLELLLLRQKLEEASQKES 504
Query: 319 E 319
+
Sbjct: 505 K 505
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 33.6 bits (78), Expect = 0.30
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 6/30 (20%)
Query: 388 GPPGVGKTSIAKSIARALNREY------FR 411
GPPG GKT++A+ +A L ++ FR
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVSAGEIFR 36
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.9 bits (75), Expect = 0.30
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 1138 VCPECKKTFSSAHHMKVHLRI--HSGIRPYKCPVEYCEKAFSTQYSRKAHI 1186
VCP C FSS+ +K H+R HS CPV C K F S H+
Sbjct: 75 VCPLCLMPFSSSVSLKQHIRYTEHS----KVCPV--CGKEFRNTDSTLDHV 119
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 33.8 bits (78), Expect = 0.30
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP GVGK +A ++A+AL
Sbjct: 19 FAGPEGVGKELLALALAKALL 39
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 35.1 bits (81), Expect = 0.31
Identities = 23/122 (18%), Positives = 53/122 (43%), Gaps = 9/122 (7%)
Query: 212 QAILEEMDIPKRLMLSLSLLKKELE------LNKLQQKIGREVEEKVKQQHRKYILQEQL 265
+ + E+++ + + L+ K EL L +L++++ +E K R L+E +
Sbjct: 332 EKLEEKLEKLESELEELAEEKNELAKLLEERLKELEERLEELEKELEKALERLKQLEEAI 391
Query: 266 KAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRN 325
+ +K+EL + I+E+ E K+ + + L E ++ LE ++
Sbjct: 392 QELKEELAELSAALEEIQEELEELEKELE---ELERELEELEEEIKKLEEQINQLESKEL 448
Query: 326 YL 327
+
Sbjct: 449 MI 450
Score = 32.8 bits (75), Expect = 1.4
Identities = 21/106 (19%), Positives = 47/106 (44%), Gaps = 8/106 (7%)
Query: 222 KRLMLSLSLLKKELE-----LNKLQQKIGR---EVEEKVKQQHRKYILQEQLKAIKKELG 273
+ + L L++ELE L +L +K+G +EE ++ L+++L+ ++K L
Sbjct: 684 EEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKELEKLEKALE 743
Query: 274 LEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSE 319
L ++ ++ + + + + + NE L+KL
Sbjct: 744 LLEELREKLGKAGLRADILRNLLAQIEAEANEILSKLSLNRYDLRR 789
Score = 32.0 bits (73), Expect = 2.5
Identities = 17/78 (21%), Positives = 42/78 (53%), Gaps = 10/78 (12%)
Query: 215 LEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGL 274
E ++ + L L L++EL K + ++ E+EE L+++L+ +++EL
Sbjct: 470 EHEKELLELYELELEELEEELSREKEEAELREEIEE----------LEKELRELEEELIE 519
Query: 275 EKDDKDAIEEKFRERIKD 292
+ ++A++E+ E+++
Sbjct: 520 LLELEEALKEELEEKLEK 537
Score = 30.5 bits (69), Expect = 6.5
Identities = 24/112 (21%), Positives = 46/112 (41%), Gaps = 11/112 (9%)
Query: 210 EQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIG-----------REVEEKVKQQHRK 258
E++ + + L L E L KL++K+ + E + R
Sbjct: 304 EEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLEERL 363
Query: 259 YILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKL 310
L+E+L+ ++KEL + +EE +E ++ +E + EEL +L
Sbjct: 364 KELEERLEELEKELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEEL 415
Score = 30.1 bits (68), Expect = 9.2
Identities = 24/113 (21%), Positives = 48/113 (42%), Gaps = 11/113 (9%)
Query: 209 TEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAI 268
E I EE + L L + E ++ +L++ RE+EE ++ L E+L+ +
Sbjct: 266 LEALKIREE----ELRELERLLEELEEKIERLEELE-REIEELEEELEGLRALLEELEEL 320
Query: 269 KKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFN 321
++L ++ + +EEK + + + E+ E+ LE E
Sbjct: 321 LEKLKSLEERLEKLEEKLEKLESELE------ELAEEKNELAKLLEERLKELE 367
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 34.6 bits (80), Expect = 0.31
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 371 AVSQLKGTTQGKI---LCFYGPPGVGKTSIAKSIARALNREYF 410
V +L L GPPG GKT+ +++AR L + +
Sbjct: 23 VVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPW 65
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 34.2 bits (79), Expect = 0.31
Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 3/78 (3%)
Query: 360 EDVKKRI-LEFIAVSQLKGT-TQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGM 417
++ K+ + A+ + G+I GP G GKT++ K +A L V G
Sbjct: 8 RNLTKKYGGDKTALDGVSFEVEPGEIFGLLGPNGAGKTTLLKILAGLLKPTSGEILVLGY 67
Query: 418 SDVAEIKGHRRTYVGAMP 435
V E RR +G +P
Sbjct: 68 DVVKEPAKVRRR-IGYVP 84
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 34.6 bits (79), Expect = 0.33
Identities = 38/177 (21%), Positives = 73/177 (41%), Gaps = 23/177 (12%)
Query: 232 KKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGL----EKDDKDAIEEKFR 287
KK L+ K + E E + + + L+E + ++ +GL E +K++ E
Sbjct: 88 KKTLQTLKPLSERLEEKESAIYEIE-SFELEEVITEPERPVGLSFEKELFEKNSFLESET 146
Query: 288 ERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQ 347
++ +K P ++ L E L + G +S+ E + +D +
Sbjct: 147 TIVRKEKDSP--LQRLGERLVREGMSQSYVEEMASKLE------------ERLSPVDQGR 192
Query: 348 AAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGK-TSIAKSIAR 403
+ + + +++R+ + G Q K++ F GP G GK TSIAK A+
Sbjct: 193 NHNVTER---AVTYLEERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAK 246
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 34.4 bits (80), Expect = 0.37
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 16/62 (25%)
Query: 357 YGMEDVKKRILEFIAVSQL----------KGTTQGKI-LCFYGPPGVGKTSIAKSIARAL 405
YG EDVKK IL QL +G I + G PG K+ + K +A+
Sbjct: 27 YGHEDVKKAIL-----LQLFGGVKKNLPDGTRLRGDINVLLVGDPGTAKSQLLKYVAKLA 81
Query: 406 NR 407
R
Sbjct: 82 PR 83
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 33.6 bits (77), Expect = 0.40
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 382 KILCFYGPPGVGKTSIAKSIARALN 406
I G PGVGKTSI+ IAR
Sbjct: 4 TIHFIGGIPGVGKTSISGYIARHRA 28
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 34.4 bits (79), Expect = 0.40
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 358 GMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
G E +KK ++ I ++L T I F GP G+GKTSIAK A+A+N
Sbjct: 20 GQELIKKILVNAILNNKL---THAYI--FSGPRGIGKTSIAKIFAKAIN 63
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 31.8 bits (73), Expect = 0.40
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 236 ELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKV 295
EL L +K+ +E+E K + + +++ + E GL ++ K + + K V
Sbjct: 2 ELEALIEKLEKEIEAARKAERAAAL--AEIRELAAEYGLTLEELLGGAAKKKAKKKRAPV 59
Query: 296 PP 297
P
Sbjct: 60 PA 61
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 34.5 bits (80), Expect = 0.40
Identities = 81/308 (26%), Positives = 116/308 (37%), Gaps = 87/308 (28%)
Query: 193 PIYLADLGAALTGAEGTEQQAILEE----MDIPKRL-MLSLSLLKKELELNKLQQKIGRE 247
P L DL + E E A+ E D +RL L L E EL L+ + +E
Sbjct: 418 PAALEDLRRRIAALE-LELDALEREAALGADHDERLAELRAELAALEAELAALEARWQQE 476
Query: 248 VEEKVKQQHRKYILQEQLKAIKKEL----GLEKDDKDAIEEKFRERIKD----KKVPPPV 299
E L E + A++ EL DD A+ + E + P V
Sbjct: 477 KE-----------LVEAILALRAELEADADAPADDDAALRAQLAELEAALASAQGEEPLV 525
Query: 300 MEVLNEELAKLGFLESHSSEFNVTRNYLDWLTSLPWG-IQSEEN---LDLTQ--AAKILD 353
++ + V DW T +P G + +E L L A +++
Sbjct: 526 FPEVDAQA--------------VAEVVADW-TGIPVGRMVRDEIEAVLSLPDRLAERVIG 570
Query: 354 DDHYGMEDVKKRILEFIAVSQLK--GTTQGKILCFYGPPGVGKTSIAKSIARALNREYFR 411
DH +E + +RI A + L+ G L GP GVGKT A ++A L Y
Sbjct: 571 QDH-ALEAIAERIR--TARAGLEDPRKPLGVFL-LVGPSGVGKTETALALAELL---Y-- 621
Query: 412 FSVGG--------MSD------VAEIKGHRRTYVGAMPGKVIQCMKKTKTE----NP--L 451
GG MS+ V+ +KG YVG G V+ TE P +
Sbjct: 622 ---GGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVL-------TEAVRRKPYSV 671
Query: 452 VLIDEVDK 459
VL+DEV+K
Sbjct: 672 VLLDEVEK 679
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 34.3 bits (79), Expect = 0.46
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 377 GTTQGKILCFYGPPGVGKTSIAKSIARAL 405
G G+ + GPPG GKT++A IAR L
Sbjct: 61 GKMAGRGILIVGPPGTGKTALAMGIAREL 89
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 33.6 bits (78), Expect = 0.46
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 381 GKILCFYGPPGVGKTSIAKSIARALNREY 409
+I F G G GKT + IAR +
Sbjct: 16 QRIGIF-GGSGTGKTVLLGMIARNAKADV 43
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 33.3 bits (77), Expect = 0.51
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 6/28 (21%)
Query: 376 KGT-TQGKILCFYGPPGVGKTSIAKSIA 402
+GT TQ YGPPG GKT+I +A
Sbjct: 22 RGTITQ-----IYGPPGSGKTNICLQLA 44
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 179
Score = 33.1 bits (76), Expect = 0.51
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGG 416
G PGVGKT++ IA L + ++ VGG
Sbjct: 12 GRPGVGKTTLVLKIAEKLREKGYK--VGG 38
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 33.2 bits (76), Expect = 0.52
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 379 TQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGM 417
T+ K++ F GPPG GK + A+ +A+ L + S G +
Sbjct: 4 TKNKVVIFLGPPGAGKGTQAERLAQELG--LKKLSTGDI 40
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 34.2 bits (78), Expect = 0.54
Identities = 16/32 (50%), Positives = 21/32 (65%)
Query: 375 LKGTTQGKILCFYGPPGVGKTSIAKSIARALN 406
LK G F+GP GVGKT+IA+ +A+ LN
Sbjct: 34 LKSGKIGHAYIFFGPRGVGKTTIARILAKRLN 65
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 33.7 bits (78), Expect = 0.54
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALN 406
+G+I GP G GK+++ K +A L
Sbjct: 27 KGEITGILGPNGSGKSTLLKCLAGLLK 53
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 32.6 bits (75), Expect = 0.54
Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 382 KILCFYGP-PGVGKTSIAKSIARALNRE 408
K++ Y P G GKT+ A ++A++L E
Sbjct: 1 KVIGVYSPVGGEGKTTFALNLAQSLAEE 28
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 34.0 bits (79), Expect = 0.54
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 387 YGPPGVGKTSIAKSIA 402
YGPPG GKT +AK++A
Sbjct: 171 YGPPGTGKTLLAKAVA 186
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 34.1 bits (79), Expect = 0.55
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 391 GVGKTSIAKSIARALN 406
GVGKT+ A+ +ARALN
Sbjct: 56 GVGKTTTARILARALN 71
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 33.7 bits (77), Expect = 0.56
Identities = 25/98 (25%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 9 SASTLISFKPLAQAPTKAAPPP---------TSPEPNKKAAKEAKIINDKMLKPKSKPLN 59
+A T +S K A+ KAA + + KKAAK+A K K +K
Sbjct: 231 AAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAVKKAAKKAAKAAAKAAKGAAKATK 290
Query: 60 GKKNAPETNQIKKGSGQGNAKSSGKSSGKPEAKSDKVV 97
GK A + K +G ++ + K K V
Sbjct: 291 GKAKAKKKAGKKAAAGSKAKATAKAPKRGAKGKKAKKV 328
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 33.8 bits (78), Expect = 0.56
Identities = 49/199 (24%), Positives = 87/199 (43%), Gaps = 36/199 (18%)
Query: 231 LKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE-R 289
LK++L +K +K+ ++EE+ +++ E + ++E EK +K +K +
Sbjct: 5 LKEKL--SKFVEKVEEKIEEEEEEE-----APEAEEEEEEEDEEEKKEKPGFFDKAKITE 57
Query: 290 IKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWLTSLPWGIQSEENLDLTQAA 349
IK+K + + EEL +L LES V L+ L +E L + +
Sbjct: 58 IKEKDIEDLL-----EEL-ELELLES-DVALEVAEEILESL---------KEKL-VGKKV 100
Query: 350 KILDD-DHYGMEDVKKRILEFIAVSQLKGTTQGK-------ILCFYGPPGVGK-TSIAKS 400
K +D + +K+ +LE ++V L + ++ F G G GK T+IAK
Sbjct: 101 KRGEDVEEIVKNALKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAK- 159
Query: 401 IARALNREYFRFSVGGMSD 419
+A L + F V D
Sbjct: 160 LAYYLKKNGFS-VVIAAGD 177
>gnl|CDD|234371 TIGR03839, termin_org_P1, adhesin P1. Members of this protein family
are the major adhesin of the Mycoplasma terminal
organelle. The protein is called adhesin P1, cytadhesin
P1, P140, attachment protein, and MgPa, with locus names
MG191 in Mycoplasma genitalium and MPN141 in M.
pneumoniae. A conserved C-terminal region is shared by
additional paralogs in M. pneumoniae and M.
gallisepticum, as well as by the member of this family
[Cell envelope, Surface structures, Cellular processes,
Pathogenesis].
Length = 1425
Score = 34.4 bits (78), Expect = 0.56
Identities = 23/134 (17%), Positives = 38/134 (28%), Gaps = 17/134 (12%)
Query: 2 FKDSDLDSASTLIS------FKPLAQAPTKAAPPPTSPE------PNKKAAKEAKIINDK 49
FK S ++ +IS + T PE PN + +
Sbjct: 1064 FKGSTTTASGAVISNWDKAGYSSRPDDSTTFNTSKILPEPFQKYKPNTSSGSTNSSPYLE 1123
Query: 50 MLKPK-----SKPLNGKKNAPETNQIKKGSGQGNAKSSGKSSGKPEAKSDKVVVSYSLWV 104
+ P N + NQ++ QG +G +G + S V S W+
Sbjct: 1124 LTAPVNVTSLDSYYVQLNNLLDPNQVRTKLRQGTTSGNGGGAGGGSSGSVNTVARVSGWL 1183
Query: 105 GSNVTAQHSINITT 118
+ S
Sbjct: 1184 VGQLPPDSSALALN 1197
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 33.7 bits (78), Expect = 0.57
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 352 LDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFR 411
+D D D L+F + + K L YG GVGK+ + +IA L ++
Sbjct: 129 IDLDDRDRLDALMAALDF--LEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVS 186
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 33.5 bits (77), Expect = 0.59
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 382 KILCFYGPPGVGKTSIAKSIARAL------NREYFRFSVGGMSDVAEIKG 425
KI+ G PG GK++ A+ A NR+ R S+ G + E K
Sbjct: 3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVNRDDLRQSLFGHGEWGEYKF 52
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 34.1 bits (79), Expect = 0.59
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 386 FYGPPGVGKTSIAKSIARALNRE 408
F G GVGKT+IA+ +A+ LN E
Sbjct: 43 FSGTRGVGKTTIARLLAKGLNCE 65
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 33.8 bits (78), Expect = 0.63
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 377 GTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
G G+ + GPPG GKT++A +I++ L +
Sbjct: 46 GKIAGRAVLIAGPPGTGKTALAIAISKELGED 77
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 31.2 bits (71), Expect = 0.71
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 383 ILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDV 420
++ G GVGKT++A ++A AL + R V + D
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKR--VLLIDDY 36
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 33.0 bits (76), Expect = 0.71
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 379 TQGKILCFYGPPGVGKTSIAKSIARALNREYFR 411
+G + G G GKT+ A+ + L +
Sbjct: 1 MKGMFIVIEGIDGAGKTTQAELLKERLEERGIK 33
>gnl|CDD|225471 COG2919, COG2919, Septum formation initiator [Cell division and
chromosome partitioning].
Length = 117
Score = 31.5 bits (72), Expect = 0.72
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 13/91 (14%)
Query: 209 TEQQAILEEMDIPKR--LMLSLSLLKKELELNKLQQKIG----REVEEKVKQQHRKYILQ 262
++ E + +R L L L L + K G +++ ++ Q +
Sbjct: 10 KQKATRQGERRVRRRRILTLVLLALLALFQYLAWFGKNGAADVLQLQRQIAAQQAEL--- 66
Query: 263 EQLKA----IKKELGLEKDDKDAIEEKFRER 289
E+L A ++ E+ KD +D IEE+ R
Sbjct: 67 EKLSARNTALEAEIKDLKDGRDYIEERARSE 97
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and metabolism].
Length = 352
Score = 33.4 bits (77), Expect = 0.73
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 360 EDVKKRILEFIAVSQLKGT-TQGKILCFYGPPGVGKTSIAKSIA 402
+V K +F AV + +G+ + GP G GKT++ + IA
Sbjct: 9 RNVSKSFGDFTAVDDISLDIKKGEFVTLLGPSGCGKTTLLRMIA 52
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 33.4 bits (77), Expect = 0.79
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 387 YGPPGVGKTSIAKSIARALNRE 408
YG G GKT++ K + + L
Sbjct: 46 YGKTGTGKTAVTKYVMKELEEA 67
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 30.6 bits (70), Expect = 0.79
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 246 REVEEKVKQQHRKYI-LQEQLKAIKKELGLEKDDKDAIEEKFRER 289
++ +++ + L+ + + ++ E+ K D D IEE+ R
Sbjct: 20 YQLNQEIAALQAELAKLKAENEELEAEVKDLKSDPDYIEERARSE 64
>gnl|CDD|179427 PRK02471, PRK02471, bifunctional glutamate--cysteine
ligase/glutathione synthetase; Provisional.
Length = 752
Score = 33.4 bits (77), Expect = 0.82
Identities = 21/139 (15%), Positives = 51/139 (36%), Gaps = 22/139 (15%)
Query: 223 RLMLSLSLLKKELELNKLQQKIGREVEEKV---------KQQHRKYILQEQLKAIKKELG 273
L L L E E ++ E + ++ + ++ + + LG
Sbjct: 307 HLFLLYLLWLDEPEDTDQWVELADENNNLIALEHPLEALALAAEAELILDAMEDLVQHLG 366
Query: 274 LEKDDKDAIEEKFRERIKDKKVPPP---VMEVLNEELAKLGFLESHSSEFNVTRNYLDWL 330
L + +D I++ +E++ D + + ++ E G + Y ++
Sbjct: 367 LPDEYQDLIKQL-KEQLTDPEKTLSGRLLKQIKQESYVAFG--------LEQAKQYKEYA 417
Query: 331 TSLPWGIQSEENLDL-TQA 348
P+ ++ E+++L TQ
Sbjct: 418 WERPYALKGYEDMELSTQI 436
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 33.2 bits (76), Expect = 0.84
Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 9/107 (8%)
Query: 224 LMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE 283
L + S + +L ++Q++I ++ +QQ ++ L++QLK+++ E+ ++E
Sbjct: 27 LAAAFSAAADDKQLKQIQKEIAALEKKIREQQDQRAKLEKQLKSLETEI-------ASLE 79
Query: 284 EKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWL 330
+ E D K + LN L L + L L
Sbjct: 80 AQLIETADDLKKLRKQIADLNARLNAL--EVQEREQRRRLAEQLAAL 124
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 32.8 bits (75), Expect = 0.85
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 10/55 (18%)
Query: 387 YGPPGVGKTSIAKSIAR-------ALNRE--YFRFSVG-GMSDVAEIKGHRRTYV 431
+G GKT+ A ++A+ L+R + + G G AE++G RR Y+
Sbjct: 7 WGATCTGKTAEAIALAKETGWPVIVLDRVQCCSQLATGSGRPLPAELQGTRRIYL 61
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 32.2 bits (74), Expect = 0.85
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 359 MEDVKKRILEFIAVSQLKGT-TQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGM 417
+E++ R A+ + T G+I+ GP G GK+++ ++IA L + G
Sbjct: 2 IENLSFRYGGRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGK 61
Query: 418 SDVAEIKGHRRTYVGAMP 435
R +G +P
Sbjct: 62 DIAKLPLEELRRRIGYVP 79
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 29.1 bits (66), Expect = 0.89
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 1138 VCPECKKTFSSAHHMKVHLR 1157
C C K F S + ++ HL+
Sbjct: 3 YCVACDKYFKSENALENHLK 22
Score = 28.7 bits (65), Expect = 1.3
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 829 CDKSFASATNYKNHMR 844
CDK F S +NH++
Sbjct: 7 CDKYFKSENALENHLK 22
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 33.0 bits (76), Expect = 0.90
Identities = 12/68 (17%), Positives = 28/68 (41%)
Query: 341 ENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKS 400
++ + + + + G + + +L GKI G GVGK+++ +
Sbjct: 124 DDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELLAGKITVLLGQSGVGKSTLINA 183
Query: 401 IARALNRE 408
+ LN++
Sbjct: 184 LLPELNQK 191
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling inter-
mediates into the (bacterio)chlorophyll branch in
response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 32.5 bits (75), Expect = 0.96
Identities = 21/46 (45%), Positives = 24/46 (52%), Gaps = 12/46 (26%)
Query: 359 MEDVK-----KRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAK 399
+ DVK KR LE IA + G G L GPPG GKT +AK
Sbjct: 2 LADVKGQEQAKRALE-IAAA---G---GHNLLMIGPPGSGKTMLAK 40
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 32.5 bits (74), Expect = 1.1
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 384 LCFYGPPGVGKTSIAKSIARALNREYFRFSVGGM 417
L F GPPG GK +IAK ++ LN Y+ S G +
Sbjct: 3 LVFLGPPGSGKGTIAKILSNELN--YYHISTGDL 34
>gnl|CDD|223079 PHA03419, PHA03419, E4 protein; Provisional.
Length = 200
Score = 32.2 bits (73), Expect = 1.1
Identities = 18/83 (21%), Positives = 26/83 (31%)
Query: 12 TLISFKPLAQAPTKAAPPPTSPEPNKKAAKEAKIINDKMLKPKSKPLNGKKNAPETNQIK 71
T F P + PPP P P D L+P +K ET +
Sbjct: 47 TGYPFCPPTTPHPSSQPPPCPPSPGHPPQTNDTHEKDLALQPPPGGKKKEKKKKETEKPA 106
Query: 72 KGSGQGNAKSSGKSSGKPEAKSD 94
+G + + K G+ D
Sbjct: 107 QGGEKPDQGPEAKGEGEGHEPED 129
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 31.4 bits (72), Expect = 1.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 381 GKILCFYGPPGVGKTSIAKSIARALN 406
G ++ G G GKT++ + IA+ L
Sbjct: 25 GDVVLLSGDLGAGKTTLVRGIAKGLG 50
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 32.3 bits (74), Expect = 1.2
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 6/97 (6%)
Query: 198 DLGAALTGAEGTEQQAILEEMDIPK------RLMLSLSLLKKELELNKLQQKIGREVEEK 251
L A E E Q E +I + R LS +K E EL L +I E
Sbjct: 46 ALEALEIELEDLENQVSQLESEIQEIRERIKRAEEKLSAVKDERELRALNIEIQIAKERI 105
Query: 252 VKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 288
+ L E+++ ++KE+ K+ + +E+ E
Sbjct: 106 NSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAE 142
>gnl|CDD|223880 COG0810, TonB, Periplasmic protein TonB, links inner and outer
membranes [Cell envelope biogenesis, outer membrane].
Length = 244
Score = 32.5 bits (74), Expect = 1.2
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 17 KPLAQAPTKAAPPPTSPEPNKKAAKEAKIINDKMLKPKSKPLNGKKNAPETNQIKK 72
+P + P PT P+P +K E K KPK KP K P+ K
Sbjct: 66 QPKPPTEPETPPEPTPPKPKEKPKPEKKP-----KKPKPKPKPKPKPKPKVKPQPK 116
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 32.8 bits (75), Expect = 1.2
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIK 424
G+ + GP G GK+++ K + R + + G+ D+ +I
Sbjct: 354 PGEKVAIVGPSGSGKSTLIKLLLRLYDPTSGEILIDGI-DIRDIS 397
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.3 bits (71), Expect = 1.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 385 CFYGPPGVGKTSIAKSIARAL 405
G PG GKT++AK +A L
Sbjct: 2 LITGTPGSGKTTLAKELAERL 22
>gnl|CDD|235958 PRK07194, fliG, flagellar motor switch protein G; Reviewed.
Length = 334
Score = 32.7 bits (75), Expect = 1.2
Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 26/88 (29%)
Query: 161 IKTVRDIISMNPLYKEQLMILLQQENSPVVDN------------------------PIYL 196
+K DII+ P ++QLM +L++ + VV+ + +
Sbjct: 199 VKQAADIINRFPGDRQQLMEMLKEHDEEVVNEIEDNMYDFFILSRQSEETLQRLMDEVPM 258
Query: 197 ADLGAALTGAEGTEQQAILEEMDIPKRL 224
AL G E +QAIL M PKR
Sbjct: 259 ELWAVALKGTEPALRQAILRVM--PKRQ 284
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 33.1 bits (76), Expect = 1.3
Identities = 16/72 (22%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 222 KRLMLSLSLLKKELE-----LNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEK 276
++L L L++ELE L +LQ+++ EE + L+E+++ ++++ +
Sbjct: 733 EQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAKLKEEIEELEEKRQALQ 792
Query: 277 DDKDAIEEKFRE 288
++ + +EE+ E
Sbjct: 793 EELEELEEELEE 804
Score = 31.2 bits (71), Expect = 4.3
Identities = 46/208 (22%), Positives = 85/208 (40%), Gaps = 46/208 (22%)
Query: 144 SLVKDLSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNP---IYLADL- 199
+K L + S + D+I +P Y+ + +L ++ VVD+ LA
Sbjct: 575 DRIKPLRSLKSDAAPGFLGLASDLIDFDPKYEPAVRFVLG--DTLVVDDLEQARRLARKL 632
Query: 200 ----------------GAALTG------------AEGTEQQAILEEMDIP-KRLMLSLSL 230
++TG E E + L E++ ++L L
Sbjct: 633 RIKYRIVTLDGDLVEPSGSITGGSRNKRSSLAQKRELKELEEELAELEAQLEKLEEELKS 692
Query: 231 LKKEL--------ELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAI 282
LK EL EL + +++ R++EE ++ EQL++ +EL E ++ +
Sbjct: 693 LKNELRSLEDLLEELRRQLEELERQLEELKRELAALEEELEQLQSRLEELEEELEELEEE 752
Query: 283 EEKFRERIKDKKVPPPVMEVLNEELAKL 310
E+ +ER+++ + +E L E LAKL
Sbjct: 753 LEELQERLEELE---EELESLEEALAKL 777
Score = 30.8 bits (70), Expect = 5.6
Identities = 26/119 (21%), Positives = 52/119 (43%), Gaps = 12/119 (10%)
Query: 226 LSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEK 285
L L + EL +LQ+++ EE + + +L+E+L+ ++ EL ++ + ++EK
Sbjct: 272 LKSELEELREELEELQEELLELKEEIEELEGEISLLRERLEELENELEELEERLEELKEK 331
Query: 286 FRERIKDKKVPPPVMEVLNEELAKL------------GFLESHSSEFNVTRNYLDWLTS 332
++ + ++E L + LA+L LE F R L L +
Sbjct: 332 IEALKEELEERETLLEELEQLLAELEEAKEELEEKLSALLEELEELFEALREELAELEA 390
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 31.8 bits (73), Expect = 1.3
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 3/60 (5%)
Query: 231 LKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERI 290
L+ E ++L+Q+I + EEK + + R L+ +L+AI+K E++++ E++ + I
Sbjct: 116 LQAEQGKSELEQEIKKLEEEKEELEKRVAELEAKLEAIEKR---EEEERQIEEKRHADEI 172
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079. This
uncharacterized family contains a P-loop.
Length = 123
Score = 31.1 bits (71), Expect = 1.3
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 374 QLKGTTQGKILCFYGPPGVGKTSIAKSIARAL 405
LK G ++ G G GKT+ + +A+ L
Sbjct: 11 LLKA---GDVVLLSGDLGAGKTTFVRGLAQGL 39
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 32.7 bits (75), Expect = 1.3
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 367 LEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSV 414
L L+G I+ YGP G GKT+ K + L V
Sbjct: 29 LASFLAPALRGERPSNIII-YGPTGTGKTATVKFVMEELEESSANVEV 75
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 31.9 bits (73), Expect = 1.4
Identities = 35/184 (19%), Positives = 75/184 (40%), Gaps = 29/184 (15%)
Query: 133 ENDDNFNDHK---VSLVKDLSEVYSALMQEVIKTVRDI-ISMNPLYKEQLMILLQQENSP 188
E D F + K + L + L ++ Q ++K R++ ++ K L+ L + E
Sbjct: 1 EEDQEFEEAKDYILKLEEQLKKLSKQA-QRLVKRRRELGSALGEFGKA-LIKLAKCEEEV 58
Query: 189 VVDNPIYLADLG------AALTGAEGTEQQAILEE---------------MDIPKRLMLS 227
+ L+ LG ++L+ A+ ++ L E +D +L+
Sbjct: 59 GGELGEALSKLGKAAEELSSLSEAQANQELVKLLEPLKEYLRYCQAVKETLDDRADALLT 118
Query: 228 LSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFR 287
L LKK+L + ++ + + + L+E+L+ + L + + I E+ +
Sbjct: 119 LQSLKKDL--ASKKAQLEKLKAAPGIKPAKVEELEEELEEAESALEEARKRYEEISERLK 176
Query: 288 ERIK 291
E +K
Sbjct: 177 EELK 180
>gnl|CDD|222689 pfam14335, DUF4391, Domain of unknown function (DUF4391). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 220 and
257 amino acids in length.
Length = 221
Score = 32.2 bits (74), Expect = 1.4
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 219 DIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 272
D+ +R+ + + E E+ KL++K+ +E KQ +RK L ++K +KKEL
Sbjct: 173 DLKERVERLEQIEELEKEIAKLKKKLKKE-----KQFNRKVELNLEIKKLKKEL 221
>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 = 32.0 bits (73), Expect = 1.4
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGM 417
GP G GK+++AK++A L Y G M
Sbjct: 9 GPSGAGKSTVAKAVAEKLG--YAYLDSGAM 36
>gnl|CDD|119417 cd00891, PI3Kc, Phosphoinositide 3-kinase (PI3K), catalytic domain;
The PI3K catalytic domain family is part of a larger
superfamily that includes the catalytic domains of other
kinases such as the typical serine/threonine/tyrosine
protein kinases (PKs), aminoglycoside
phosphotransferase, choline kinase, and RIO kinases.
PI3Ks catalyze the transfer of the gamma-phosphoryl
group from ATP to the 3-hydroxyl of the inositol ring of
D-myo-phosphatidylinositol (PtdIns) or its derivatives.
PI3Ks play an important role in a variety of fundamental
cellular processes, including cell motility, the Ras
pathway, vesicle trafficking and secretion, immune cell
activation and apoptosis. They can be divided into three
main classes (I, II, and III), defined by their
substrate specificity, regulation, and domain structure.
Class I PI3Ks are the only enzymes capable of converting
PtdIns(4,5)P2 to the critical second messenger
PtdIns(3,4,5)P3. Class I enzymes are heterodimers and
exist in multiple isoforms consisting of one catalytic
subunit (out of four isoforms) and one of several
regulatory subunits. Class II PI3Ks comprise three
catalytic isoforms that do not associate with any
regulatory subunits. They selectively use PtdIns as a
susbtrate to produce PtsIns(3)P.
Length = 352
Score = 32.6 bits (75), Expect = 1.5
Identities = 12/46 (26%), Positives = 27/46 (58%)
Query: 228 LSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELG 273
S L K++E+ + + ++V+ + + RK +L+E+LK ++ L
Sbjct: 1 RSELLKQVEVINELKTLAKKVKREKSKSQRKELLREELKKLENNLP 46
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 32.3 bits (74), Expect = 1.5
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 384 LCFYGPPGVGKTSIAKSIARAL 405
L +G G GKT +A IA L
Sbjct: 117 LLLWGSVGTGKTYLAACIANEL 138
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 31.8 bits (73), Expect = 1.5
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 17/87 (19%)
Query: 222 KRLMLSLSLLKKELELNKLQQKI------------GREVEEKV-KQQHRKYILQEQLKAI 268
+L L LKKELE +L+Q+I GRE E+ + L+++LK +
Sbjct: 65 NKLKTRLEKLKKELE--ELKQRIAELQAQIEKLKKGREETEERTELLEELKQLEKELKKL 122
Query: 269 KKELG-LEKDDKDAIEEKFRERIKDKK 294
K EL EK+D + IE+ +E K K
Sbjct: 123 KAELEKYEKNDPERIEKL-KEETKVAK 148
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 32.5 bits (74), Expect = 1.6
Identities = 16/30 (53%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 380 QGKILCFYGPPGVGK-TSIAKSIARALNRE 408
QG +L GP GVGK T+ AK AR + RE
Sbjct: 184 QGGVLALVGPTGVGKTTTTAKLAARCVARE 213
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 31.6 bits (72), Expect = 1.6
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 377 GTTQGKILCFYGPPGVGKTSIA 398
G +G I YGPPG GKT+I
Sbjct: 8 GVERGTITQIYGPPGSGKTNIC 29
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 32.5 bits (74), Expect = 1.6
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP GVGKTS A+ +A+A+N
Sbjct: 43 FTGPRGVGKTSTARILAKAVN 63
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 32.5 bits (74), Expect = 1.7
Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 4/92 (4%)
Query: 8 DSASTLISFKPLAQAPTKAAPPPTSPEPNKKAAKEAKIINDKMLKPKSKPLNGKKNAPET 67
++ L + +K SPE K+AK+ + + + K++ K A
Sbjct: 149 AASPALKPTANGKRPSSKPPKSIMSPEVKVKSAKKTQDTSKETTTEKTEGKTSVKAASLK 208
Query: 68 NQIKKGSGQGNAKSSGKSSGKPEAKSDKVVVS 99
+ + N SS K + K +K S
Sbjct: 209 ---RNPPKKSNIMSSFFKK-KTKEKKEKKEAS 236
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 31.7 bits (72), Expect = 1.7
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 377 GTTQGKILCFYGPPGVGKTSIAKSIA 402
G +G + YGPPG GKT+IA +A
Sbjct: 15 GVERGTVTQVYGPPGTGKTNIAIQLA 40
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 32.3 bits (74), Expect = 1.8
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKTS A+ +AR+LN
Sbjct: 42 FSGPRGCGKTSSARILARSLN 62
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 31.9 bits (73), Expect = 1.8
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 360 EDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSI 401
ED+ + ++E + L+ + ++ G GVGKT++AK I
Sbjct: 2 EDMIEALIEKL----LEMSDNLGVVGIVGMGGVGKTTLAKQI 39
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 27.9 bits (63), Expect = 1.9
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 1139 CPECKKTFSSAHHMKVHLR 1157
C C TF+S +K HLR
Sbjct: 3 CELCNVTFTSESQLKSHLR 21
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 32.0 bits (73), Expect = 1.9
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 388 GPPGVGKTSIAKSIARALN 406
G GVGK++IA +AR L
Sbjct: 96 GASGVGKSTIAGELARRLG 114
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 31.7 bits (72), Expect = 1.9
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 360 EDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNR 407
+ V R L ++ G + GP G GKT++A +AR +R
Sbjct: 8 KRVTSRALRYLKS--------GYPVHLRGPAGTGKTTLAMHVARKRDR 47
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 30.6 bits (70), Expect = 2.0
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 383 ILCFYGPPGVGKTSIAKSIARALNREY---FRFSV 414
++ GP GVGK+++ K L E+ F FSV
Sbjct: 1 LIVLSGPSGVGKSTLLK----RLLEEFDPNFGFSV 31
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 32.2 bits (73), Expect = 2.0
Identities = 34/157 (21%), Positives = 56/157 (35%), Gaps = 22/157 (14%)
Query: 210 EQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIK 269
+ +E + LSLL + K+ + + L+ +
Sbjct: 246 LRSVRIEVSSASHEFIEDLSLLLLRFG-----------IVSKIYRSTLIISGKRNLENFR 294
Query: 270 KELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDW 329
K +G +K EK E+ K + P +NEEL +L L F TRN L
Sbjct: 295 KYIGFSVKEKAEALEKIIEKSKKSERYP-----INEELKRLRLL------FGFTRNELSS 343
Query: 330 LTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRI 366
+SEE +IL+ G +++ K+I
Sbjct: 344 NIPFYSKYESEEAPSYEILMEILNSIERGSKNLDKKI 380
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 32.1 bits (73), Expect = 2.1
Identities = 14/21 (66%), Positives = 15/21 (71%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKTS+AK A ALN
Sbjct: 45 FSGPRGTGKTSVAKIFANALN 65
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 31.4 bits (72), Expect = 2.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 388 GPPGVGKTSIAKSIARALNREYF 410
GP G GK+++AK +A L Y
Sbjct: 11 GPAGSGKSTVAKILAEKLGFHYL 33
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 30.1 bits (68), Expect = 2.1
Identities = 10/42 (23%), Positives = 15/42 (35%)
Query: 3 KDSDLDSASTLISFKPLAQAPTKAAPPPTSPEPNKKAAKEAK 44
+ D+D + P A A AA + A EA+
Sbjct: 46 EGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAE 87
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 32.3 bits (74), Expect = 2.2
Identities = 21/119 (17%), Positives = 52/119 (43%), Gaps = 15/119 (12%)
Query: 216 EEMDIPKRLMLSLSLLKKELELNK---------LQQKIGREVEEKVKQQHRKYILQEQLK 266
EE++ ++ + +L+ LE K L++++ + + + + L E+L
Sbjct: 281 EEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELA 340
Query: 267 AIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRN 325
++++L K++ +++E + E + +E EEL + LE+ S+
Sbjct: 341 ELEEKLEELKEELESLEAELEELEAEL----EELESRLEELEEQ--LETLRSKVAQLEL 393
>gnl|CDD|227293 COG4957, COG4957, Predicted transcriptional regulator
[Transcription].
Length = 148
Score = 30.8 bits (70), Expect = 2.2
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 1128 VKKSTSSENNVCPECKKTFSSAHHMKVHLRIHSGIRP------YKCPVEY 1171
+KKS + + +C E K F S +K HL H G+ P + P +Y
Sbjct: 68 IKKSVTPDYIICLEDGKKFKS---LKRHLTTHYGLTPDEYRAKWGLPPDY 114
>gnl|CDD|227084 COG4741, COG4741, Predicted secreted endonuclease distantly related
to archaeal Holliday junction resolvase [Nucleotide
transport and metabolism].
Length = 175
Score = 30.9 bits (70), Expect = 2.2
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 3/71 (4%)
Query: 224 LMLSLSLLKKELELNKLQQKI---GREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKD 280
+L+L L + LQ K+ RE+EE +++ R+ ++ E ++E L++ +
Sbjct: 11 FILALVLYLLRAYIRSLQGKVESKARELEETLQKAERERLVNEAQARKEEEWKLKEWIEK 70
Query: 281 AIEEKFRERIK 291
IEE + ++
Sbjct: 71 KIEEAREDAVR 81
>gnl|CDD|197874 smart00787, Spc7, Spc7 kinetochore protein. This domain is found
in cell division proteins which are required for
kinetochore-spindle association.
Length = 312
Score = 31.5 bits (72), Expect = 2.3
Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 232 KKELELNKLQQKIG---REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE----- 283
EL++ ++K+ +E+ KVK+ L+E+L+ ++ ++ + K +
Sbjct: 201 CDPTELDRAKEKLKKLLQEIMIKVKKLE---ELEEELQELESKIEDLTNKKSELNTEIAE 257
Query: 284 -EKFRERIKD 292
EK E+ +
Sbjct: 258 AEKKLEQCRG 267
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 31.7 bits (72), Expect = 2.6
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKT+IA+ +A+ LN
Sbjct: 43 FAGPRGTGKTTIARILAKVLN 63
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 30.6 bits (70), Expect = 2.6
Identities = 7/22 (31%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 382 KILCFYGPPGVGKTSIAKSIAR 403
+I G P GKT++ +++A
Sbjct: 1 RI-VITGGPSTGKTTLLEALAA 21
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 31.7 bits (72), Expect = 2.7
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 358 GMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
G + VKK I+ + + + I F GP G GKT++A+ +A++LN E
Sbjct: 18 GQDHVKKLIINAL---KKNSISHAYI--FAGPRGTGKTTVARILAKSLNCE 63
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 30.9 bits (71), Expect = 2.7
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGH-RRTYVGAMPGKV 438
G+I+ GP G GK+++ K++A L + G D+A + + +P
Sbjct: 24 AGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGK-DLASLSPKELARKIAYVP--- 79
Query: 439 IQCMKKTKTEN 449
Q ++ +
Sbjct: 80 -QALELLGLAH 89
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 31.3 bits (71), Expect = 2.8
Identities = 33/102 (32%), Positives = 48/102 (47%), Gaps = 18/102 (17%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRF---SVGGMSDVAEI----KGH------RRTYVGAM 434
GPP VGKT++ + IAR L+ +F VG + + +EI G RR V
Sbjct: 144 GPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDP 203
Query: 435 PGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEML 476
K M ++ +P V+I VD+IG + A A+L L
Sbjct: 204 CPKAEGMMMAIRSMSPEVII--VDEIGT---EEDALAILTAL 240
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 31.9 bits (73), Expect = 2.8
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 386 FYGPPGVGKTSIAKSIARAL 405
F GP GVGKT +AK++A L
Sbjct: 600 FLGPTGVGKTELAKALAEFL 619
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 31.8 bits (72), Expect = 2.8
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP G GKTS A+ +AR+LN
Sbjct: 40 FSGPRGCGKTSSARILARSLN 60
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 31.5 bits (72), Expect = 2.9
Identities = 41/263 (15%), Positives = 95/263 (36%), Gaps = 55/263 (20%)
Query: 371 AVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTY 430
AV++ G + YG G+GKT + ++I V ++ +
Sbjct: 104 AVAENPGGAYNPLF-IYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFT----NDF 158
Query: 431 VGAMPGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLD 490
V A+ ++ K+ + + L+LID++ + H +
Sbjct: 159 VKALRDNEMEKFKEKYSLD-LLLIDDIQFLAGKERTQEE---------------FFHTFN 202
Query: 491 VPVDLS-RVLFICTA--NVIDTIPEPLRDRMEM---IDVSGYVAEEKVAIAAQYLIPQAM 544
++ +++ ++ + + LR R+E +++ E ++AI +
Sbjct: 203 ALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAIL------RKK 256
Query: 545 KESGLSPEQITLEPSAIQVLIKNYCRESGVRNLQKHIEKV-----TRKVALTI------- 592
E I + ++ L K R VR L+ + ++ K A+TI
Sbjct: 257 AED----RGIEIPDEVLEFLAKRLDRN--VRELEGALNRLDAFALFTKRAITIDLVKEIL 310
Query: 593 --VKKESDKVTVTNDNLSDFVGK 613
+ + +K+T+ +++ V +
Sbjct: 311 KDLLRAGEKITI--EDIQKIVAE 331
>gnl|CDD|188164 TIGR01751, crot-CoA-red, crotonyl-CoA reductase. The enzyme
modelled by This model is responsible for the conversion
of crotonyl-CoA reductase to butyryl-CoA. In serine
cycle methylotrophic bacteria this enzyme is involved in
the process of acetyl-CoA to glyoxylate. In other
bacteria the enzyme is used to produce butyrate for
incorporation into polyketides such as tylosin from
Streptomyces fradiae and coronatine from Pseudomonas
syringae.
Length = 398
Score = 31.7 bits (72), Expect = 2.9
Identities = 20/105 (19%), Positives = 38/105 (36%), Gaps = 22/105 (20%)
Query: 715 AMTGEISLVGKVLPVGGI--KEKTIAAKRVGVHTIL----------MPEENKKDFTDLPE 762
+ +++ G PV + EK + +G ++ +P+ N + + +
Sbjct: 204 SYATQLARAGGGNPVAVVSSPEKAEYCRSLGAEAVIDRNDFGHWGRLPDHNTQAPKEWTK 263
Query: 763 YIREGLNVHFVSEWRQVY-----DLVFEHTSERPFPCPVLGCDRS 802
+ F R++ D+VFEH FP V C R
Sbjct: 264 SFKR-----FGKRIRELTGGEDPDIVFEHPGRATFPTSVYVCRRG 303
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 31.0 bits (70), Expect = 3.0
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 229 SLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 288
S +KK E N L V++K K+ K LQ++L+ +KKEL E +D+ I+ +
Sbjct: 90 SHIKKHKERNTLPDL--NNVDKKTKKLINK--LQKELEELKKELDNEMNDELTIQPIHDK 145
Query: 289 RIKDKKVPPPVMEVLNEELAKL 310
I K V E +E+ +L
Sbjct: 146 IIIKKDENNSVSE--HEDFKQL 165
>gnl|CDD|193532 cd05656, M42_Frv, M42 Peptidase, Endoglucanases. Peptidase M42
family, Frv (Frv Operon Protein; Endo-1
4-Beta-Glucanase; Cellulase Protein; Endoglucanase;
Endo-1 4-Beta-Glucanase Homolog; Glucanase; EC. 3.2.1.4)
subfamily. Frv is a co-catalytic metallopeptidase, found
in archaea and bacteria, including Pyrococcus horikoshii
tetrahedral shaped phTET1 (DAPPh1; FrvX; PhDAP
aminopeptidase; PhTET aminopeptidase; deblocking
aminopeptidase), phTET2 (DAPPh2) and phTET3 (DAPPh3),
Haloarcula marismortui TET (HmTET) as well as Bacillus
subtilis YsdC. All of these exhibit aminopeptidase and
deblocking activities. The HmTET is a broad substrate
aminopeptidase capable of degrading large peptides.
PhTET2, which shares 24% identity with HmTET, is a
cobalt-activated peptidase and possibly a deblocking
aminopeptidase, assembled as a 12-subunit tetrahedral
dodecamer, while PhTET1 can be alternatively assembled
as a tetrahedral dodecamer or as an octahedral
tetracosameric structure. The active site in such a
self-compartmentalized complex is located on the inside
such that substrate sizes are limited, indicating
function as possible peptide scavengers. PhTET2 cleaves
polypeptides by a nonprocessive mechanism, preferring
N-terminal hydrophobic or uncharged polar amino acids.
The YsdC gene is conserved in a number of thermophiles,
archaea and pathogenic bacterial species; the closest
structural homolog is Thermotoga maritima FrwX (34%
identity), which is annotated as either a cellulase or
an endoglucanase, and is possibly involved in
polysaccharide biosynthesis or degradation.
Length = 336
Score = 31.3 bits (72), Expect = 3.1
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 19/57 (33%)
Query: 725 KVLPVGGIKEKTIAAKRVGVHT---------------ILMPEENKK--DFTDLPEYI 764
+ PVGG+ + + +RV +HT +L PEE KK DL +I
Sbjct: 78 RFSPVGGVDPRVLLGQRVRIHTKKGEVPGVIGSKPPHLLKPEERKKVPKIDDL--FI 132
>gnl|CDD|200530 cd11269, Sema_6D, The Sema domain, a protein interacting module, of
semaphorin 6D (Sema6D). Sema6D is expressed
predominantly in the nervous system during embryogenesis
and it uses Plexin-A1 as a receptor. It displays
repellent activity for dorsal root ganglion axons.
Sema6D also acts as a regulator of late phase primary
immune responses. In addition, Sema6D is overexpressed
in gastric carcinoma, indicating that it may have an
important role in the occurrence and development of the
cancer. Sema6D is a member of the class 6 semaphorin
family of proteins, which are membrane associated
semaphorins. Semaphorins are regulatory molecules
involved in the development of the nervous system and in
axonal guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 465
Score = 31.5 bits (71), Expect = 3.1
Identities = 35/137 (25%), Positives = 57/137 (41%), Gaps = 19/137 (13%)
Query: 280 DAIEEKFRERIKDKKVPPPVMEVLNEE---------LAKLGFLESHSSEFNVTRNYLDWL 330
D IE+ F+ R K++K P V + E+ AK G E++ + + L ++
Sbjct: 286 DDIEKVFKGRFKEQKTPDSVWTAVPEDKVPKPRPGCCAKHGLAEAYKTSIDFPDETLSFI 345
Query: 331 TSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGP- 389
S P L + I+++ + V+ R L IAV G Q + F G
Sbjct: 346 KSHP--------LMDSAVPSIIEEPWFTKTRVRYR-LTAIAVDHAAGPHQNYTVIFVGSE 396
Query: 390 PGVGKTSIAKSIARALN 406
GV +AK+ +LN
Sbjct: 397 AGVVLKILAKTSPFSLN 413
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 31.6 bits (72), Expect = 3.3
Identities = 12/23 (52%), Positives = 18/23 (78%)
Query: 386 FYGPPGVGKTSIAKSIARALNRE 408
F G GVGKT++A+ +A++LN E
Sbjct: 43 FTGTRGVGKTTLARILAKSLNCE 65
>gnl|CDD|179392 PRK02249, PRK02249, DNA primase large subunit; Validated.
Length = 343
Score = 31.1 bits (71), Expect = 3.3
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 282 IEEKFRERIKDK---KVPPPVMEVLNEELAKL 310
+ E RERI D VP + E L L ++
Sbjct: 170 LREAIRERILDGLPLAVPEEIAEALLPLLEEI 201
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 30.4 bits (68), Expect = 3.4
Identities = 19/64 (29%), Positives = 36/64 (56%)
Query: 231 LKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERI 290
L++E E + +++ RE EEK K++ + QEQ + + + E+ + A EE R R+
Sbjct: 69 LRREEEARRQEEERAREKEEKAKRKAEEEEKQEQEEQERIQKQKEEAEARAREEAERMRL 128
Query: 291 KDKK 294
+ +K
Sbjct: 129 EREK 132
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 30.5 bits (69), Expect = 3.4
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFR 411
+GP G GKT++A +A + + +
Sbjct: 4 VFGPTGSGKTTLALQLALNIATKGGK 29
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 31.4 bits (72), Expect = 3.4
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 391 GVGKTSIAKSIARALNREYFR---FSVG 415
G GKT++ + RAL R + F VG
Sbjct: 11 GSGKTTVTLGLMRALRRRGLKVQPFKVG 38
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.5 bits (72), Expect = 3.7
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 368 EFIAVSQLKGTTQGKI----LCFYGPPGVGKTSIAKSIARALN 406
E IA + +I L F GP G GKTS A+ +A++LN
Sbjct: 22 EAIATTLKNALISNRIAPAYL-FTGPRGTGKTSSARILAKSLN 63
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 30.9 bits (71), Expect = 3.8
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 381 GKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVG 432
G+I+ G G GKT++ K+I + R G D+ + H R +G
Sbjct: 29 GEIVALLGRNGAGKTTLLKTIMGLVRPRSGRIIFDG-EDITGLPPHERARLG 79
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 31.5 bits (72), Expect = 3.8
Identities = 34/199 (17%), Positives = 73/199 (36%), Gaps = 40/199 (20%)
Query: 150 SEVYSALMQEVIKTVRDIISMNPLYKEQL--MILLQQENSPVVDNPIYLADLGAALTGAE 207
E Y L++++ + + S E+L ++ ++ENS + +L A L E
Sbjct: 277 DEEYQELIEQLEELIDKYESHIEKALEELESILDTEKENSEFKL---DVEELKALLEALE 333
Query: 208 ---GTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEE---------KVKQQ 255
Q + E++ P + S+ +N + I + E K K +
Sbjct: 334 EILEKNLQKLEEKLKDPSTSIELESITDLIESINDIIDAINELIREHNEKIDNLKKEKNK 393
Query: 256 HRKYI--------------LQEQLKAIKKELGLEKDDKDAIEE---KFRERIKDKK---- 294
+K + Q++ K ++K + + + +E + IK+ +
Sbjct: 394 AKKKLWLHLVAELKEDIDAYQKEKKGLEKAINSLEKEIKQLEAEIKALEKEIKELEKQLT 453
Query: 295 -VPPPVMEVLNEELAKLGF 312
+ P + +N+ L GF
Sbjct: 454 NIEPTA-DEINKLLKAYGF 471
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 261
Score = 31.0 bits (70), Expect = 3.8
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 383 ILCFYGPPGVGKTSIAKSIARALNRE 408
++ G PG GKT+ AK +A+ L +E
Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQE 28
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 30.7 bits (70), Expect = 3.8
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 359 MEDVKKRILEFIAVSQLKGTTQGKILCFY-GPPGVGKTSIAKSIARALNRE 408
+E V K +L +A Q + Q + + GPPG GK+++A+ + L ++
Sbjct: 12 IEAVHKPLLRRLAALQAEP--QRRTIVGIAGPPGAGKSTLAEFLEALLQQD 60
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 31.0 bits (71), Expect = 4.0
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 367 LEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
L F L+G+ +L YGPPG GKT+ K + L
Sbjct: 42 LAFALRPALRGSRPLNVLI-YGPPGTGKTTTVKKVFEELEEI 82
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 31.3 bits (71), Expect = 4.1
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F GP GVGKT+ A+ A+ +N
Sbjct: 44 FCGPRGVGKTTCARIFAKTIN 64
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 230
Score = 30.8 bits (69), Expect = 4.2
Identities = 17/52 (32%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 354 DDHYGMEDVKKRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARAL 405
D+ ++ KR+L L+ L FYGPPGVGKT+ R +
Sbjct: 1 DELVPWQEAVKRLLVQA----LESGRLPHALLFYGPPGVGKTTAPPKNTRFI 48
>gnl|CDD|234348 TIGR03761, ICE_PFL4669, integrating conjugative element protein,
PFL_4669 family. Members of this protein family, such
as PFL4669, are found in integrating conjugative
elements (ICE) of the PFGI-1 class as in Pseudomonas
fluorescens.
Length = 216
Score = 30.3 bits (69), Expect = 4.2
Identities = 9/45 (20%), Positives = 23/45 (51%)
Query: 128 MQMAAENDDNFNDHKVSLVKDLSEVYSALMQEVIKTVRDIISMNP 172
+ A+E DD + D + +++ MQ +++ + D+++ P
Sbjct: 47 INQASEQDDPYADWALLRIEEKLLSARQEMQALLQRLDDLLAQLP 91
>gnl|CDD|173302 PRK14841, PRK14841, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 233
Score = 30.7 bits (69), Expect = 4.3
Identities = 25/98 (25%), Positives = 46/98 (46%), Gaps = 12/98 (12%)
Query: 212 QAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKE 271
Q I EM++ +R + + +L ++ L + K +EVEEK K+ R ++ I
Sbjct: 77 QMIDREMELLRRERVRVRILGRKEGLPEKVLKKWQEVEEKTKEFDRMTLV------IAFN 130
Query: 272 LGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAK 309
G ++ DA+E ++ + KK+ L EE +
Sbjct: 131 YGGRREILDAVESILKDVSQGKKI------ELTEETFR 162
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 30.9 bits (70), Expect = 4.3
Identities = 33/116 (28%), Positives = 55/116 (47%), Gaps = 21/116 (18%)
Query: 386 FYGPPGVGKTSIAKSIARALNREY-------------FRFSVGGMSDVAEIKGHRRTYVG 432
G GVGKT+IA+ +A++LN + G D+ EI RT V
Sbjct: 43 LSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVE 102
Query: 433 AMPGKVIQCMKKT--KTENPLVLIDEVDKIGKGYSGDPASALLEML-DPEQNANFL 485
M +++ + + K+ + LIDEV + + +S +ALL+ L +P Q+ F+
Sbjct: 103 EMR-EILDNIYYSPSKSRFKVYLIDEVHMLSR-HS---FNALLKTLEEPPQHIKFI 153
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 31.1 bits (71), Expect = 4.4
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 246 REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNE 305
E+EE++++++ + +LK + E + + +K +E+K ++ IK K + E L E
Sbjct: 64 EEIEEELREEYEE-----ELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLE 118
Query: 306 ELA 308
A
Sbjct: 119 LEA 121
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 30.0 bits (68), Expect = 4.7
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 384 LCFYGPPGVGKTSIAKSIARAL 405
+ G G GKT++ + IA
Sbjct: 3 VILQGEAGSGKTTLLQKIALLW 24
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 30.9 bits (69), Expect = 4.7
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 386 FYGPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKT 445
G G GK IA+ IA AL+ ++ + + + D E+KG ++ A +
Sbjct: 124 LKGGAGSGKNHIAEQIAEALDLDF--YFMNAIMDEFELKG----FIDANGKFHETPFYEA 177
Query: 446 KTENPLVLIDEVD 458
+ L IDE+D
Sbjct: 178 FKKGGLFFIDEID 190
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 31.2 bits (71), Expect = 4.8
Identities = 19/73 (26%), Positives = 42/73 (57%), Gaps = 8/73 (10%)
Query: 229 SLLKKELELNKLQQKIGREVEEKVKQQHRKYI----LQEQLKAIKKELGLEKDDKDAIEE 284
L + E+N++ ++ E+ E++++ ++ L+E+++ ++KEL + K +EE
Sbjct: 201 ELEEVLREINEISSEL-PELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLEE 259
Query: 285 KFRE---RIKDKK 294
K RE RI++ K
Sbjct: 260 KIRELEERIEELK 272
Score = 30.8 bits (70), Expect = 6.4
Identities = 20/100 (20%), Positives = 47/100 (47%), Gaps = 18/100 (18%)
Query: 228 LSLLKKELE-----LNKLQQKIGREVEEKVKQQH------------RKYILQEQLKAIKK 270
L+ +K LE L +L++K E E++++++ L+++ + IKK
Sbjct: 635 LAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAELEELEKRREEIKK 694
Query: 271 ELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEELAKL 310
L K++ + E+ ++ ++ + +E L E++ K
Sbjct: 695 TLEKLKEELEEREKA-KKELEKLEKALERVEELREKVKKY 733
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 30.6 bits (69), Expect = 4.9
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 384 LCFYGPPGVGKTSIAKSIARALN 406
L F GP GVGKT+ A+ +AR +N
Sbjct: 42 LLFCGPRGVGKTTCARILARKIN 64
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 30.7 bits (69), Expect = 5.0
Identities = 28/118 (23%), Positives = 48/118 (40%), Gaps = 24/118 (20%)
Query: 176 EQLMILLQQENSPVVDNPIYLADLGAALTG--AEGTEQQAILEEMDIPKRL--------- 224
+ L +L + + + G L G E Q+ +LE + ++
Sbjct: 130 QGLAVLERSRGGQLYGKLLRFDSNGQELDGDPLERELQKRLLEVETLRDQVDKMVEQQVR 189
Query: 225 MLS-----LSLLKKELELN-----KLQQKIGREVEEKVKQQHRKYILQEQLKAIKKEL 272
+++ L L K+ L+LN + QQ V EK + Q R LQ +L A++ EL
Sbjct: 190 VINSQLERLRLEKRRLQLNGQLDDEFQQHY---VAEKSELQKRLAQLQTELDALRAEL 244
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 30.1 bits (69), Expect = 5.0
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 359 MEDVKKRILEFIAVS--------QLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
+E +K +AVS +L+ +GK G GVGK+++ ++ L
Sbjct: 55 LEIYEKLGYPVLAVSAKTGEGLDELRELLKGKTSVLVGQSGVGKSTLLNALLPELVLA 112
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 30.1 bits (68), Expect = 5.2
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 388 GPPGVGKTSIAKSIARALNREY 409
G PGVGKT+++K +A L EY
Sbjct: 7 GTPGVGKTTVSKLLAEKLGYEY 28
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 31.0 bits (70), Expect = 5.3
Identities = 21/101 (20%), Positives = 50/101 (49%), Gaps = 9/101 (8%)
Query: 686 VKKDGPSAGITITTALVSLA---TGKPIKQNLAMTGEISLVGKVLPVGGIKEKTIAAKRV 742
+ K+G + I +++ + K + + L GE++L GK+ + G+ A++
Sbjct: 69 LPKEGGRFDLPIAIGILAASEQLDAKNLGEYL-FLGELALDGKLRGIKGVLPAIALAQKS 127
Query: 743 GVHTILMPEENKKDFTDLPEYIREGLNVHFVSEWRQVYDLV 783
G I++P+EN ++ + + +GLN++ ++V +
Sbjct: 128 GRKFIIVPKENAEEAS-----LIDGLNIYGADHLKEVVKFL 163
>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 257 to 277 amino acids in length. This domain is
found associated with pfam00004. This domain has a
conserved LER sequence motif.
Length = 276
Score = 30.5 bits (69), Expect = 5.3
Identities = 25/105 (23%), Positives = 44/105 (41%), Gaps = 24/105 (22%)
Query: 204 TGAEGTEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQE 263
T E T+Q+ + L+ +KELE + Q EE +K Q + QE
Sbjct: 97 TLQEQTQQEQQRAQYQDE----LARKRYQKELEQQRRQN------EELLKMQEESVLRQE 146
Query: 264 QL-------------KAIKKELGLE-KDDKDAIEEKFRERIKDKK 294
+ + I++E LE ++ + IE + R R K+++
Sbjct: 147 AMRRATEEEILEMRRETIEEEAELERENIRAKIEAEARGRAKEER 191
>gnl|CDD|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201). This is
a family of coiled-coil proteins from eukaryotes. The
function is not known.
Length = 177
Score = 29.9 bits (68), Expect = 5.4
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 14/81 (17%)
Query: 222 KRLMLS--LSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELG------ 273
K ML L LKKEL+ + + R+ KVK + K L++Q K ++++ G
Sbjct: 85 KLHMLEEELERLKKELKEKEERLAKLRKELYKVKLERDK--LRKQNKKLRQQGGLLHVPA 142
Query: 274 LEKD---DKDAIEEKFRERIK 291
L D + +EEK R+ ++
Sbjct: 143 LLYDYDKTVEKVEEK-RKSVE 162
>gnl|CDD|220640 pfam10234, Cluap1, Clusterin-associated protein-1. This protein is
conserved from worms to humans. The protein of 413 amino
acids contains a central coiled-coil domain, possibly
the region that binds to clusterin. Cluap1 expression is
highest in the nucleus and gradually increases during
late S to G2/M phases of the cell cycle and returns to
the basal level in the G0/G1 phases. In addition, it is
upregulated in colon cancer tissues compared to
corresponding non-cancerous mucosa. It thus plays a
crucial role in the life of the cell.
Length = 269
Score = 30.4 bits (69), Expect = 5.4
Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 22/101 (21%)
Query: 230 LLKKELELNKLQQKIGR------EVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIE 283
LL KEL+L + +QK EVE+ +K+ + L +L+ ++ EL K D+ +E
Sbjct: 141 LLGKELDLRESRQKALSRPLELAEVEKALKEAIKN--LAARLQQLQAELDNLKSDEANLE 198
Query: 284 EKFR------ERIKD-----KKVPPPVM---EVLNEELAKL 310
K ER + + V P M E L EEL KL
Sbjct: 199 AKIERKKQELERTQKRLQALQSVRPAFMEEYEKLEEELQKL 239
>gnl|CDD|238997 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a
conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase activity
by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its DNA
binding sites. Increasing the fraction of ParA-ADP in
the cell inhibits cell division, suggesting that this
simple nucleotide switch may regulate cytokinesis. ParA
shares sequence similarity to a conserved and widespread
family of ATPases which includes the repA protein of the
repABC operon in R. etli Sym plasmid. This operon is
involved in the plasmid replication and partition.
Length = 104
Score = 28.7 bits (65), Expect = 5.5
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 13/39 (33%)
Query: 370 IAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
IAV+ KG GVGKT+ A ++A AL R
Sbjct: 2 IAVANQKG-------------GVGKTTTAVNLAAALARR 27
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 30.3 bits (69), Expect = 5.5
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 16/69 (23%)
Query: 340 EENLDLTQAAKILDDDHYGMEDVKKRIL--EFIAVSQLKGTTQGKILCFYGPPGVGKTSI 397
E +++ +K H ++DV I E +A+ GP G GK+++
Sbjct: 1 EMMIEVKNLSKTYPGGHQALKDVNLEINQGEMVAI--------------IGPSGAGKSTL 46
Query: 398 AKSIARALN 406
+S+ ++
Sbjct: 47 LRSLNGLVD 55
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and repair].
Length = 226
Score = 30.2 bits (69), Expect = 5.6
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 371 AVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNR 407
A+ QL + L +G G GK+ + ++ A
Sbjct: 28 ALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEE 64
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 30.0 bits (68), Expect = 5.7
Identities = 8/47 (17%), Positives = 22/47 (46%)
Query: 246 REVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIKD 292
E E +++Q + + +L+A ++ L K+ + + + + I
Sbjct: 49 AEAEREIEQLREQELSSAKLEAKRERLNARKEVLEDVRNQVEDEIAS 95
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 30.8 bits (69), Expect = 5.7
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 375 LKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
LK T K + GPPGVGKT +A+ +A L E
Sbjct: 188 LKRLTIKKNIILQGPPGVGKTFVARRLAYLLTGE 221
>gnl|CDD|219741 pfam08193, INO80_Ies4, INO80 complex subunit Ies4. The INO80
ATPase is a member of the SNF2 family of ATPases and
functions as an integral component of a multisubunit
ATP-dependent chromatin remodelling complex. This family
of proteins corresponds to the fungal Ies4 subunit of
INO80.
Length = 228
Score = 30.4 bits (68), Expect = 5.8
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 16/91 (17%)
Query: 3 KDSDLDSASTLISFKPLAQAPTKAAPPPTSPEPNKKAAKEAKIINDKMLKPKSKPLNGKK 62
+D DS ++ + P+ + A+ ++P A P+ K G K
Sbjct: 43 EDEPSDSPASSAADPPVPSSVDNASDAASTPAAGTSATD----------TPRRKGGPGPK 92
Query: 63 NAPETNQIKKGSGQG-NAKSSGKSSGKPEAK 92
K+ +GQG ++++ K GKP K
Sbjct: 93 KG-----EKRSAGQGTTSETTSKPRGKPGPK 118
>gnl|CDD|201447 pfam00794, PI3K_rbd, PI3-kinase family, ras-binding domain.
Certain members of the PI3K family possess Ras-binding
domains in their N-termini. These regions show some
similarity (although not highly significant similarity)
to Ras-binding pfam00788 domains (unpublished
observation).
Length = 107
Score = 28.8 bits (65), Expect = 5.8
Identities = 18/100 (18%), Positives = 28/100 (28%), Gaps = 21/100 (21%)
Query: 574 VRNLQKHIEKVTRKVALTI-VKKESDKVTVTNDNLSDFVGKPIFSHDRLFEITPPGVVTR 632
+ + + L I V E ++T T F P +
Sbjct: 2 SKVSPEPLPNKLINNKLLIVVHLEGKQMTKT------------------FTCNPNSTPGQ 43
Query: 633 KVALTIVKKESDKVTVTNDNLSDFVGKPIFSHDRLFEITP 672
+A + KK V D D+V K + L P
Sbjct: 44 LIAQALRKK--LSVLDQGDVTDDYVLKVCGRDEYLLGDHP 81
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 29.6 bits (67), Expect = 5.8
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNR 407
+G + F G G GK++IA ++ R L
Sbjct: 1 RGCTIWFTGLSGSGKSTIANALERKLFA 28
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 30.0 bits (68), Expect = 5.8
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 382 KILCFYGPPGVGKTSIAKSIAR 403
++ G PGVGKT++ K +
Sbjct: 1 MLIAITGTPGVGKTTVCKLLRE 22
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 30.1 bits (68), Expect = 5.9
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 14/101 (13%)
Query: 232 KKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRERIK 291
+ +LE K ++ RE EE+ +++ +K + + + ++E E+ +K EE+ +ER +
Sbjct: 8 RAKLEE-KQARRQQREAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEERKEREE 66
Query: 292 DKKVPPPVMEVLNEELAKLGFLESHSSEFNVTRNYLDWLTS 332
+ EE KL S F V D L++
Sbjct: 67 QARKE-------QEEYEKL------KSSFVVEEEGTDKLSA 94
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 30.1 bits (69), Expect = 6.3
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIA 402
+G+I+ G G GKT++ K+I
Sbjct: 25 EGEIVALLGRNGAGKTTLLKTIM 47
>gnl|CDD|234818 PRK00708, PRK00708, sec-independent translocase; Provisional.
Length = 209
Score = 29.8 bits (67), Expect = 6.4
Identities = 22/55 (40%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 17 KPLAQAP---TKAAPPPTSPEPNKKAAKEA---KIINDKMLKPKSKPLNGKKNAP 65
KP A++P KAAP PT KKA K A K DK P K KK
Sbjct: 155 KPRAKSPRPAAKAAPKPTETITAKKAKKTAAAPKPTADKTATPAKKTTKKKKTKA 209
>gnl|CDD|226631 COG4152, COG4152, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 300
Score = 30.0 bits (68), Expect = 6.7
Identities = 19/66 (28%), Positives = 25/66 (37%), Gaps = 1/66 (1%)
Query: 360 EDVKKRILEFIAVSQLK-GTTQGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMS 418
E V K + AV + G+I GP G GKT+ + I L + G
Sbjct: 6 EGVTKSFGDKKAVDNISFEVPPGEIFGLLGPNGAGKTTTFRMILGLLEPTEGEITWNGGP 65
Query: 419 DVAEIK 424
EIK
Sbjct: 66 LSQEIK 71
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 30.4 bits (68), Expect = 6.8
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F G GVGKT+IA+ A+ALN
Sbjct: 43 FSGTRGVGKTTIARIFAKALN 63
>gnl|CDD|223918 COG0849, ftsA, Cell division ATPase FtsA [Cell division and
chromosome partitioning].
Length = 418
Score = 30.3 bits (69), Expect = 6.8
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 542 QAMKESGLSPEQITLEP--SAIQVLIKNYCRESGV 574
+ ++ +GL + I LEP SA+ VL ++ +E GV
Sbjct: 172 KCVERAGLKVDNIVLEPLASALAVLTEDE-KELGV 205
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 30.2 bits (68), Expect = 6.8
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 372 VSQLKGTTQGKILCFYGPPGVGKTSIAKSIARALNRE 408
S T + K++ GP G GK+ +A +A+ LN E
Sbjct: 12 GSGASKTKKEKVIVISGPTGAGKSRLALELAKRLNGE 48
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 30.1 bits (69), Expect = 6.9
Identities = 39/150 (26%), Positives = 63/150 (42%), Gaps = 56/150 (37%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRT---YVG----AMPGKVIQ 440
GP G GKT +A+++AR L+ F+ ++D + T YVG + K++Q
Sbjct: 115 GPTGSGKTLLAQTLARILD---VPFA---IADATTL-----TEAGYVGEDVENILLKLLQ 163
Query: 441 -C-MKKTKTENPLVLIDEVDKIGKGYSGDPAS------------ALLEMLD--------- 477
K + +V IDE+DKI + + S ALL++L+
Sbjct: 164 AADYDVEKAQRGIVYIDEIDKIAR--KSENPSITRDVSGEGVQQALLKILEGTVASVPPQ 221
Query: 478 -----PEQNANFLDHYLDVPVDLSRVLFIC 502
P+Q + VD + +LFIC
Sbjct: 222 GGRKHPQQEF--------IQVDTTNILFIC 243
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 29.6 bits (67), Expect = 7.0
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 20/97 (20%)
Query: 209 TEQQAILEEMDIPKRLMLSL-----SLLKKELELNKLQQKIGREVEEKVKQQHRKY---- 259
T+ EE+ KR + S+ +L K+ E ++ ++ ++ +E +K+ + Y
Sbjct: 75 TKDSEEKEEL---KRTLQSMKSRLKTLKNKDRE-REILKEHKKQEKELIKEGKKPYYLKK 130
Query: 260 --ILQEQLKAIKKELGLEKDDKDAIEEKFRERIKDKK 294
I + LK EL K +K E+ + K
Sbjct: 131 SEIKKLVLKKKFDELKKSKQ-----LDKALEKKRKKN 162
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 30.1 bits (68), Expect = 7.0
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 7/72 (9%)
Query: 233 KELELNKLQQKIGREVEE----KVKQQHRKYILQEQLKAIKKELGLEKDDKDAIEEKFRE 288
+ E N Q++ + ++E K+KQQ +K +E+ + +K+ E++ K EE +++
Sbjct: 169 AKPERNVSQEEAKKRLQEWELKKLKQQQQKR--EEERRKQRKKQQEEEERKQKAEEAWQK 226
Query: 289 RIKD-KKVPPPV 299
+K+ K+ P PV
Sbjct: 227 WMKNVKQRPKPV 238
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 29.5 bits (67), Expect = 7.1
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 388 GPPGVGKTSIAKSIARALNREY-----FRFSVGGMSDVAEI 423
G G GKT++ ++A+AL + + S M+ VAEI
Sbjct: 9 GARGCGKTTVGMALAQALGYRFVDTDQWLQSTSNMT-VAEI 48
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 30.6 bits (69), Expect = 7.3
Identities = 50/234 (21%), Positives = 92/234 (39%), Gaps = 43/234 (18%)
Query: 149 LSEVYSALMQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLGAALTGAEG 208
L E L +E K M+P+ E++ L + N + P YL+ L L
Sbjct: 484 LQERLENLREEFSKANSQDQLMHPVLMEKIEKLKDEFNKRLSRAPNYLS-LKYKLD---- 538
Query: 209 TEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAI 268
+L E K L E +K+ E+ +K K+ + ++E+++A+
Sbjct: 539 -----MLNEFSRAKALS----------EKKSKAEKLKAEINKKFKEVMDRPEIKEKMEAL 583
Query: 269 KKELGLEKDDK-DAIEEKFRERIKDKKVPPPVMEVLNEELAKLGFLESHSSEFN-VTRNY 326
K E+ D +++ +E+++ K + + ELA + L+S E VT+
Sbjct: 584 KAEVASSGASSGDELDDDLKEKVEKMK------KEIELELAGV--LKSMGLEVIGVTKKN 635
Query: 327 LDWLTSLPWGIQSEENLDLTQAAKILDDDHYGMEDVKKRILEFIAVSQLKGTTQ 380
D P +L + + L+ E++ K+I I S LK +
Sbjct: 636 KDTAEQTP-------PPNLQEKIESLN------EEINKKIERVIRSSDLKSKIE 676
>gnl|CDD|151277 pfam10828, DUF2570, Protein of unknown function (DUF2570). This is
a family of proteins with unknown function.
Length = 110
Score = 28.7 bits (64), Expect = 7.7
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 209 TEQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAI 268
+ Q I ++ +RL +L ++E + + QQKI E+E K ++ E++K I
Sbjct: 36 AQAQTIEQQQKANQRLTDAL---EQERQAVEEQQKIANEIERKAEEN------AEEVKTI 86
Query: 269 KKE 271
K+
Sbjct: 87 LKQ 89
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 30.5 bits (69), Expect = 7.8
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 386 FYGPPGVGKTSIAKSIARALNRE 408
F G GVGKTS+A+ A+ LN E
Sbjct: 43 FTGTRGVGKTSLARLFAKGLNCE 65
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 29.7 bits (68), Expect = 7.8
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSV 414
+G ++ GP G GK+++ K++ + SV
Sbjct: 4 RGLLIVLSGPSGAGKSTLVKALLERDPN--LQLSV 36
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 30.4 bits (69), Expect = 7.9
Identities = 39/137 (28%), Positives = 54/137 (39%), Gaps = 32/137 (23%)
Query: 388 GPPGVGKTSIAKSIARALNREYFRFSVGGMSDVAEIKGHRRTYVGAMPGKVIQCMKKTKT 447
G G GK+ AK+IA R VG + I VG ++ Q ++ +
Sbjct: 266 GIQGTGKSLTAKAIANDWQLPLLRLDVGKL--FGGI-------VGESESRMRQMIRIAEA 316
Query: 448 ENPLVL-IDEVDKI-----GKGYSGDPASALLEMLD--PEQNANFLDHYLDVPVDLSRVL 499
+P +L IDE+DK KG SG L + E+ S V
Sbjct: 317 LSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKK--------------SPVF 362
Query: 500 FICTANVIDTIP-EPLR 515
+ TAN ID +P E LR
Sbjct: 363 VVATANNIDLLPLEILR 379
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 30.2 bits (68), Expect = 8.0
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 386 FYGPPGVGKTSIAKSIARALN 406
F G GVGKT++++ +A++LN
Sbjct: 43 FTGTRGVGKTTLSRILAKSLN 63
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 29.9 bits (68), Expect = 8.0
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 5/37 (13%)
Query: 382 KILCFYGPPGVGKTSIAKSIARALNR-----EYFRFS 413
+I G PG GK+++ K I E+ S
Sbjct: 31 RIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFLHCS 67
>gnl|CDD|131526 TIGR02473, flagell_FliJ, flagellar export protein FliJ. Members of
this family are the FliJ protein found, in nearly every
case, in the midst of other flagellar biosynthesis genes
in bacgterial genomes. Typically the fliJ gene is found
adjacent to the gene for the flagellum-specific ATPase
FliI. Sequence scoring in the gray zone between trusted
and noise cutoffs include both probable FliJ proteins
and components of bacterial type III secretion systems.
Length = 141
Score = 28.8 bits (65), Expect = 8.3
Identities = 23/120 (19%), Positives = 49/120 (40%), Gaps = 22/120 (18%)
Query: 157 MQEVIKTVRDIISMNPLYKEQLMILLQQENSPVVDNPIYLADLGAALTGAEGTEQQAILE 216
Q + + + Y+E+ QQ V GA + E + Q +
Sbjct: 25 AQAEFERLETQLQQLIKYREEYE---QQALEKV----------GAGTSALELSNYQRFIR 71
Query: 217 --EMDIPKRLMLSLSLLKKELE--LNKLQQK-IGREVEEKVKQQHRKYILQEQLKAIKKE 271
+ I ++ L+LL++E+E +L + + EK+K++ +K + + + K+E
Sbjct: 72 QLDQRI-QQQQQELALLQQEVEAKRERLLEARRELKALEKLKEKKQK---EYRAEEAKRE 127
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 28.8 bits (65), Expect = 8.4
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 211 QQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKK 270
Q+ +E+ P + LK E E NK ++K R E+K +++ RK +Q K K
Sbjct: 71 QRQAAKEVKKPGISTKAQQALKLEHERNKQEKKK-RSKEKKEEEKERKR-QLKQQKKKAK 128
>gnl|CDD|216531 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family. This
family consists of the 116kDa V-type ATPase (vacuolar
(H+)-ATPases) subunits, as well as V-type ATP synthase
subunit i. The V-type ATPases family are proton pumps
that acidify intracellular compartments in eukaryotic
cells for example yeast central vacuoles,
clathrin-coated and synaptic vesicles. They have
important roles in membrane trafficking processes. The
116kDa subunit (subunit a) in the V-type ATPase is part
of the V0 functional domain responsible for proton
transport. The a subunit is a transmembrane glycoprotein
with multiple putative transmembrane helices it has a
hydrophilic amino terminal and a hydrophobic carboxy
terminal. It has roles in proton transport and assembly
of the V-type ATPase complex. This subunit is encoded by
two homologous gene in yeast VPH1 and STV1.
Length = 707
Score = 30.0 bits (68), Expect = 8.4
Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 227 SLSLLKKELELNKLQQKIGREVEEKVKQ-QHRKYILQEQLKAIKKELGLEKDDKDAIEEK 285
S L E E+ L+ +I +EVEE ++ + L+E L + +E ++ + + E
Sbjct: 66 SKEFLDLEEEILDLEAEI-KEVEENLESLEKEINELEEWLNVLDEEKSFLDENLEELSEL 124
Query: 286 FR 287
Sbjct: 125 SN 126
>gnl|CDD|219580 pfam07793, DUF1631, Protein of unknown function (DUF1631). The
members of this family are sequences derived from a
group of hypothetical proteins expressed by certain
bacterial species. The region concerned is approximately
440 amino acid residues in length.
Length = 729
Score = 30.3 bits (69), Expect = 8.8
Identities = 12/61 (19%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 247 EVEEKVKQQHRKYILQEQLKAIKKELGLEKDD--KDAIEEKFRERIKDKKVPPPVMEVLN 304
E + ++Q+ R+ L EQ + + E G + + + ++++ +R+ + +P V+ +L
Sbjct: 453 EFQAFLEQERRRSELVEQ-RTREAEEGRARLELARQQVQQELEQRLAGRSLPEVVVTLLR 511
Query: 305 E 305
+
Sbjct: 512 Q 512
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 30.1 bits (69), Expect = 8.8
Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 232 KKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIKKELGLEK-----DDKDAIEEKF 286
+ LE + K+ E E++++++ + E+ + ++KE L++ + ++ EK
Sbjct: 57 EALLEAKEEIHKLRNEFEKELRERRNELQKLEK-RLLQKEENLDRKLELLEKREEELEKK 115
Query: 287 RERIKDKKVPPPVMEVLNEELAKL 310
+ ++ K+ +E EEL +L
Sbjct: 116 EKELEQKQQ---ELEKKEEELEEL 136
>gnl|CDD|213232 cd03265, ABC_DrrA, Daunorubicin/doxorubicin resistance ATP-binding
protein. DrrA is the ATP-binding protein component of a
bacterial exporter complex that confers resistance to
the antibiotics daunorubicin and doxorubicin. In
addition to DrrA, the complex includes an integral
membrane protein called DrrB. DrrA belongs to the ABC
family of transporters and shares sequence and
functional similarities with a protein found in cancer
cells called P-glycoprotein. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region in
addition to the Walker A motif/P-loop and Walker B motif
commonly found in a number of ATP- and GTP-binding and
hydrolyzing proteins.
Length = 220
Score = 29.6 bits (67), Expect = 8.9
Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 360 EDVKKRILEFIAVSQLKGTT-QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGMS 418
E++ K+ +F AV + +G+I GP G GKT+ K + L R +V G
Sbjct: 4 ENLVKKYGDFEAVRGVSFRVRRGEIFGLLGPNGAGKTTTIKMLTTLLKPTSGRATVAGHD 63
Query: 419 DVAEIKGHRRT--YVGAMP 435
V E + RR V
Sbjct: 64 VVREPREVRRRIGIVFQDL 82
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 30.1 bits (68), Expect = 8.9
Identities = 38/130 (29%), Positives = 57/130 (43%), Gaps = 24/130 (18%)
Query: 505 NVIDTIPEPLRDRMEMIDVSGYVAEEKVAIAAQYLIPQAMKESGLSPEQITLEPSAIQVL 564
NV+ PLR+R E I + A+ + + +E+G +T+ PSAI+VL
Sbjct: 360 NVVPIFLPPLRERREDI-----------PLLAEAFLEKFNRENGRP---LTITPSAIRVL 405
Query: 565 IKNYCRESG-VRNLQKHIEK-VTRKVALTIVKKESDKVTVTNDNLSDFVGKP----IFSH 618
+ C+ G VR L+ +E+ T + TI SD + LS + K S
Sbjct: 406 MS--CKWPGNVRELENCLERTATLSRSGTIT--RSDFSCQSGQCLSPMLAKTCPHGHISI 461
Query: 619 DRLFEITPPG 628
D L TPP
Sbjct: 462 DPLAGTTPPH 471
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 9.1
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 382 KILCFYGPPGVGKTSIAKSIARALNREYFRFSVGGM 417
+ GPPG GK+++AK +A+ L G +
Sbjct: 1 MRILILGPPGAGKSTLAKKLAKKL--GLPHLDTGDI 34
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family for
which functions are known are part of an exonuclease
complex with sbcD homologs. This complex is involved in
the initiation of recombination to regulate the levels
of palindromic sequences in DNA. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1042
Score = 30.3 bits (68), Expect = 9.3
Identities = 12/42 (28%), Positives = 17/42 (40%)
Query: 364 KRILEFIAVSQLKGTTQGKILCFYGPPGVGKTSIAKSIARAL 405
K + + T G I G G GKT++ +I AL
Sbjct: 9 KNFGSYKGTHTIDFTALGPIFLICGKTGAGKTTLLDAITYAL 50
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 29.9 bits (68), Expect = 9.5
Identities = 21/97 (21%), Positives = 48/97 (49%), Gaps = 13/97 (13%)
Query: 210 EQQAILEEMDIPKRLMLSLSLLKKELELNKLQQKIGREVEEKVKQQHRKYILQEQLKAIK 269
E++ I E +R + + ++ L + ++ RE + K +++ + +LQEQ++
Sbjct: 28 EKKRIKAEEKEEERRIDEMMEEERLKALAEEEE---RERKRKEERREGRAVLQEQIEE-- 82
Query: 270 KELGLEKDDKDAIEEKFRERIKDKKVPPPVMEVLNEE 306
EK ++ EE+ +ER + + ++E + EE
Sbjct: 83 ----REKRRQEEYEERLQEREQMDE----IIERIQEE 111
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system belong
to the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. Functionally, this transport system is involved
in osmoregulation. Under conditions of stress, the
organism recruits these transport system to accumulate
glycine betaine and other solutes which offer
osmo-protection. It has been demonstrated that glycine
betaine uptake is accompanied by symport with sodium
ions. The locus has been named variously as proU or
opuA. A gene library from L.lactis functionally
complements an E.coli proU mutant. The comlementing
locus is similar to a opuA locus in B.sutlis. This
clarifies the differences in nomenclature [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 363
Score = 29.8 bits (67), Expect = 9.6
Identities = 24/116 (20%), Positives = 46/116 (39%), Gaps = 10/116 (8%)
Query: 380 QGKILCFYGPPGVGKTSIAKSIARALNREYFRFSVGG-----MSDVAEIKGHRRTYVGAM 434
+G+I G G GK++ + + R + + + G S V E++ RR +G +
Sbjct: 18 KGEIFVIMGLSGSGKSTTVRMLNRLIEPTAGQIFIDGENIMKQSPV-ELREVRRKKIGMV 76
Query: 435 PGKVIQCMKKTKTENPLVLIDEVDKIGKGYSGDPASALLEMLDPEQNANFLDHYLD 490
+ T +N L E+ + + A LL+++ E + Y D
Sbjct: 77 FQQFALFPHMTILQN-TSLGPELLGWPEQERKEKALELLKLVGLE---EYEHRYPD 128
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
0.315 0.132 0.378
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 61,893,678
Number of extensions: 6225432
Number of successful extensions: 8713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8581
Number of HSP's successfully gapped: 447
Length of query: 1230
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1122
Effective length of database: 6,147,370
Effective search space: 6897349140
Effective search space used: 6897349140
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 (21.6 bits)
S2: 65 (28.7 bits)