RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780784|ref|YP_003065197.1| polynucleotide
phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str.
psy62]
(699 letters)
>gnl|CDD|183327 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 1121 bits (2903), Expect = 0.0
Identities = 373/693 (53%), Positives = 509/693 (73%), Gaps = 2/693 (0%)
Query: 1 MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60
MF+ IE+ GR L LETG++ARQ++GAVL YG+TVVL TVV + K+GQDFFPLT
Sbjct: 1 MFNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLT 60
Query: 61 VNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQH 120
V+Y+E+TYA GKIPGG+ +RE RP+E E L SR+IDR IRPLF K ++NE QV+ V+
Sbjct: 61 VDYEEKTYAAGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSV 120
Query: 121 DLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVS 179
D E+ P +++M+ ASAAL +SG+PF GP+ +V YI+G++VLNP ++E ++ LDL V+
Sbjct: 121 DPENDPDILAMIGASAALSISGIPFNGPIAAVRVGYIDGEFVLNPTVEELEESDLDLVVA 180
Query: 180 GTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSK 239
GT+DAVLMVE EA +LSE+V+L+AI FGH + +I+A +LA + + +
Sbjct: 181 GTKDAVLMVESEAKELSEEVMLEAIEFGHEAIQELIDAQEELAAEAGPKWEWQPPEVDEE 240
Query: 240 LEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSS-EHSSWNEGEIVSVFEDI 298
L+ + ++ + L+ + I +K R +D +K++++ ++ E +E EI F+ +
Sbjct: 241 LKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFKKL 300
Query: 299 QAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRE 358
+ K+VR +L++ +R+DGR + +R IS +VG+L RTHGS+LF RG+TQA+VV TLGT
Sbjct: 301 EKKIVRRRILEEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVATLGTLR 360
Query: 359 DEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQ 418
DEQ +D L G + FM+HYNF P + GE R+G+P RREIGHG LA RA+ PVLP +
Sbjct: 361 DEQIIDGLEGEYKKRFMLHYNFPPYSVGETGRVGSPGRREIGHGALAERALEPVLPSEEE 420
Query: 419 FPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSD 478
FPYT+R+VSEI ES+GSSSMA+VCGSSLALMDAGVPI PVAGIAMGL+K+GD + +L+D
Sbjct: 421 FPYTIRVVSEILESNGSSSMASVCGSSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLTD 480
Query: 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKV 538
I GDEDHLG MDFKVAGT GITA+QMD+KI GI+ I+ AL+QAK GRLHIL +M++
Sbjct: 481 ILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREILEEALEQAKEGRLHILGKMNEA 540
Query: 539 LSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS 598
+SE R +L + PR+E + IPPD+IR+VIG GGK IR I E+TGAK++I+DDGTVKIA++
Sbjct: 541 ISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAAT 600
Query: 599 SLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA 658
EAA+E I IT PEV +IY+G+VV+++DFGAFV +DGLVHIS+++ ERV
Sbjct: 601 DGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVE 660
Query: 659 KTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVD 691
K DV+KEGD V VK+L+ D RG+I+LS K V
Sbjct: 661 KVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAVL 693
>gnl|CDD|163340 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family).
Length = 684
Score = 1058 bits (2738), Expect = 0.0
Identities = 393/687 (57%), Positives = 505/687 (73%), Gaps = 14/687 (2%)
Query: 10 EWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYA 69
E+ GR L LETG+IARQ+DGAV+ YG+TVVL TVV + K+GQDFFPLTVNYQE+ YA
Sbjct: 1 EYGGRTLTLETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLTVNYQEKFYA 60
Query: 70 VGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVV 129
GKIPGG+ +RE RP+E E L SR+IDR IRPLF K ++NE QV+ V+ +D E+ P ++
Sbjct: 61 AGKIPGGFFKREGRPSEKETLTSRLIDRPIRPLFPKGFRNEVQVVATVLSYDPENDPDIL 120
Query: 130 SMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVSGTQDAVLMV 188
+++ ASAAL +SG+PF GP+ +V YI+GQYVLNP +DE ++ LDL V+GT+DAVLMV
Sbjct: 121 AIIGASAALAISGIPFNGPIAAVRVGYIDGQYVLNPTVDELEKSDLDLVVAGTKDAVLMV 180
Query: 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMI 248
E EA +LSE+V+L AI FGH E +PVIEAI +LA+ KE + + ++EE+ +
Sbjct: 181 ESEAKELSEEVMLGAIEFGHEEIQPVIEAIEELAEEAGKEKWEFVAPE---VDEELKAKV 237
Query: 249 KEDLRVSCF-----IPEKYVRCKQIDDLKKKMVSYF----SSEHSSWNEGEIVSVFEDIQ 299
KE + I EK R +D +K++++ E + E EI F+D++
Sbjct: 238 KELAYEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEEEEEEEADREKEIKEAFKDLE 297
Query: 300 AKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRED 359
K+VR +L + R+DGRD +T+R IS +VG+L RTHGS+LF RG+TQA+VV TLGT D
Sbjct: 298 KKIVRERILKEGKRIDGRDLDTIRPISIEVGVLPRTHGSALFTRGETQALVVTTLGTERD 357
Query: 360 EQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQF 419
EQ +D L G R FM+HYNF P + GEV R+G P RREIGHG LA RA+ VLP +F
Sbjct: 358 EQIIDDLEGEYRKRFMLHYNFPPYSVGEVGRVGGPGRREIGHGALAERALKAVLPSEEEF 417
Query: 420 PYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDD-FIILSD 478
PYT+R+VSEI ES+GSSSMA+VCG SLALMDAGVPI PVAGIAMGL+K+GD+ F +LSD
Sbjct: 418 PYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDERFAVLSD 477
Query: 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKV 538
I GDEDHLG MDFKVAGT GITA+QMD+KI GI+ IM AL+QAK GRLHIL EM+KV
Sbjct: 478 ILGDEDHLGDMDFKVAGTRDGITALQMDIKIDGITREIMEQALEQAKEGRLHILGEMNKV 537
Query: 539 LSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS 598
+SE R +L + PR+E + I PD+IR+VIG GGKVIR I E+TGAK++I+DDGTVKIA+S
Sbjct: 538 ISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAAS 597
Query: 599 SLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA 658
EAA +MI IT PEV KIY+G+VV++MDFGAFV +DGLVHIS+++ ERV
Sbjct: 598 DGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVE 657
Query: 659 KTSDVVKEGDTVWVKLLDFDDRGKIKL 685
K DV+KEGD V VK+L+ D +G+IKL
Sbjct: 658 KVEDVLKEGDEVKVKVLEIDKQGRIKL 684
>gnl|CDD|177797 PLN00207, PLN00207, polyribonucleotide nucleotidyltransferase;
Provisional.
Length = 891
Score = 599 bits (1546), Expect = e-172
Identities = 297/756 (39%), Positives = 448/756 (59%), Gaps = 64/756 (8%)
Query: 5 HTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQ 64
+V+I R + +ETG I RQ+ G+V T GET+V +V + DFFPL+V+YQ
Sbjct: 80 FSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQ 139
Query: 65 ERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLES 124
ER A G+ GG+ +RE R ++E+LI R+IDR +RP K + +ETQ++ V+ +D
Sbjct: 140 ERFSAAGRTSGGFFKREGRTKDHEVLICRLIDRPLRPTMPKGFYHETQILSWVLSYDGLH 199
Query: 125 SPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVSGTQD 183
SP +++ AA A+ LS +P + G +V I G++++NP E ++ LDL ++GT
Sbjct: 200 SPDSLAVTAAGIAVALSEVPNLKAIAGVRVGLIGGKFIVNPTTKEMEESELDLIMAGTDS 259
Query: 184 AVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFS--KLE 241
A+LM+E N L E+ +L+A+ G + + + + I L K C K P ++D+ +L
Sbjct: 260 AILMIEGYCNFLPEEKLLEAVEVGQDAVRAICKEIEVLVKKCGK-PKMLDAIKLPPPELY 318
Query: 242 EEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVS------YFSSEHSS---------- 285
+ + ++ ++L + I K R K + L++K++S Y S + S
Sbjct: 319 KHVKEIAGDELVKALQIRGKIPRRKALSSLEEKVLSILTEEGYVSKDESFGTSETRADLL 378
Query: 286 ----WNEGEIVS-----------------------------VFEDIQAKVVRTVMLDKKV 312
+E +V VF+++ +K +R +++
Sbjct: 379 EDEDEDEEVVVDGEVDEGDVHIKPIPRKSSPLLFSEVDVKLVFKEVTSKFLRRRIVEGGK 438
Query: 313 RMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQR- 371
R DGR + +R I++ GLL R HGS+LF RG+TQA+ VVTLG ++ Q +D+L
Sbjct: 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVTLGDKQMAQRIDNLVDADEV 498
Query: 372 NDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITE 431
F + Y+F P GEV R+GAPSRREIGHG LA RA+ P+LP FPYT+R+ S ITE
Sbjct: 499 KRFYLQYSFPPSCVGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITE 558
Query: 432 SDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDF------IILSDISGDEDH 485
S+GSSSMA+VCG LAL DAGVP+ P+AGIAMG+V D ++F +ILSDI+G ED
Sbjct: 559 SNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMGMVLDTEEFGGDGSPLILSDITGSEDA 618
Query: 486 LGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQ 545
G MDFKVAG + GITA QMD+K+GGI+ IM AL QAK GR HIL EMSK +
Sbjct: 619 SGDMDFKVAGNEDGITAFQMDIKVGGITLPIMERALLQAKDGRKHILAEMSKCSPPPSKR 678
Query: 546 LGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAK-VNIDDDGTVKIASSSLAEIE 604
L ++ P + IM + P+++ +IG GGK ++ I+E+TG + ++ DDGTVKI + L+ +E
Sbjct: 679 LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLE 738
Query: 605 AAREMIRSITDVPEVNKIYKGQVVKVM-DFGAFVHFCGARDGLVHISQLSTERVAKTSDV 663
++ +I S+T VP V IY+ +K + +GAFV R+GL HIS+LS+ +AK D
Sbjct: 739 KSKAIISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDA 798
Query: 664 VKEGDTVWVKLLDFDDRGKIKLSMK--VVDQNTGKP 697
K GD + VKL++ +D+G+++LS + + + N+ K
Sbjct: 799 FKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKS 834
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al.
present characterization of two proteins from
Streptomyces coelicolor. The protein in this family was
shown to have poly(A) polymerase activity and may be
responsible for polyadenylating RNA in this species.
Reference 2 showed that a nearly identical
plasmid-encoded protein from Streptomyces antibioticus
is a bifunctional enzyme that acts also as a guanosine
pentaphosphate synthetase.
Length = 719
Score = 562 bits (1450), Expect = e-160
Identities = 289/705 (40%), Positives = 434/705 (61%), Gaps = 37/705 (5%)
Query: 14 RPLKLETGRIARQSDGAVLATY-GETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGK 72
R ++ ETGR+ARQ+ G+V+A ET++L+ + KD DFFPLTV+ +ER YA G+
Sbjct: 17 RTIRFETGRLARQAAGSVVAYLDDETMLLSATTASKQPKDQFDFFPLTVDVEERMYAAGR 76
Query: 73 IPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSMV 132
IPG + RRE RP+ + IL R+IDR +RP F K +NE QV++ V+ + + VV++
Sbjct: 77 IPGSFFRREGRPSTDAILTCRLIDRPLRPSFVKGLRNEVQVVVTVLSLNPDHLYDVVAIN 136
Query: 133 AASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSL-DLFVSG----TQD-AVL 186
AASA+ L+GLPF GP+ G +V I+GQ+V P ++ +G++ D+ V+G D A++
Sbjct: 137 AASASTQLAGLPFSGPIGGVRVALIDGQWVAFPTHEQLEGAVFDMVVAGRVLENGDVAIM 196
Query: 187 MVELEANQLSEDVVLDA--------IIFGHNECKPVIEAISK----LAKMCAKE----PI 230
MVE EA + + D+V + G KP I+ + + LA+ AK P+
Sbjct: 197 MVEAEATEKTWDLVKGGAEAPTEEVVAEGLEAAKPFIKVLCRAQADLAEKAAKPTGEFPL 256
Query: 231 VIDSKDFSKLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGE 290
D +D + E + +K++L + I K R + +D++K + + + + E E
Sbjct: 257 FPDYQD--DVYEAVEGAVKDELSAALTIAGKQEREEALDEVKALVAAKLAEQFEG-REKE 313
Query: 291 IVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIV 350
I + + + K+VR +L + VR+DGR +R + A+V ++ R HGS+LF RG+TQ +
Sbjct: 314 ISAAYRAVTKKLVRERVLTEGVRIDGRGVTDIRPLDAEVQVIPRVHGSALFERGETQILG 373
Query: 351 VVTLGTREDEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIH 410
V TL + EQ +DSLS +M HYNF P +TGE R+G+P RREIGHG LA RA+
Sbjct: 374 VTTLNMLKMEQQIDSLSPETSKRYMHHYNFPPYSTGETGRVGSPKRREIGHGALAERALV 433
Query: 411 PVLPQTAQFPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDG 470
PVLP +FPY +R VSE S+GS+SM +VC S+L+L++AGVP+ PVAGIAMGL+ D
Sbjct: 434 PVLPSREEFPYAIRQVSEALGSNGSTSMGSVCASTLSLLNAGVPLKAPVAGIAMGLISDE 493
Query: 471 DD----FIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKR 526
D ++ L+DI G ED G MDFKVAGT +TA+Q+D K+ GI +++ AL+QA+
Sbjct: 494 VDGETRYVALTDILGAEDAFGDMDFKVAGTSEFVTALQLDTKLDGIPASVLASALKQARD 553
Query: 527 GRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVN 586
RL IL+ M++ + ++ ++ + PR+ + IP D+I VIG GK+I I ++TGA+++
Sbjct: 554 ARLAILDVMAEAI-DTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEIS 612
Query: 587 IDDDGTVKIASSSLAEIEAAREMIRSITD--VPEVNKIYKGQVVKVMDFGAFVHFCGARD 644
I+DDGTV I ++ EAAR MI +I + +PEV + + G VVK FGAFV +D
Sbjct: 613 IEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKD 672
Query: 645 GLVHISQLST----ERVAKTSDVVKEGDTVWVKLLDFDDRGKIKL 685
GL+HISQ+ +RV DV+ G + V++ D DDRGK+ L
Sbjct: 673 GLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSL 717
>gnl|CDD|179695 PRK03983, PRK03983, exosome complex exonuclease Rrp41; Provisional.
Length = 244
Score = 109 bits (274), Expect = 3e-24
Identities = 76/245 (31%), Positives = 122/245 (49%), Gaps = 15/245 (6%)
Query: 307 MLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSL 366
+L+ +R+DGR + +R I +VG+L+ GS+ G+ + I V G RE + L
Sbjct: 9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV-YGPRE--MHPRHL 65
Query: 367 SGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYT-LRI 425
R + YN P + E R G P RR I ++ R A+ P + FP T + +
Sbjct: 66 QLPDRAVLRVRYNMAPFSVDERKRPG-PDRRSIEISKVIREALEPAI-MLELFPRTVIDV 123
Query: 426 VSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDH 485
E+ ++D + +A + +SLAL DAG+P+ VAG A+G V D I+L D++ +ED+
Sbjct: 124 FIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV---DGVIVL-DLNKEEDN 179
Query: 486 LGHMDFKVAGTDSG--ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESR 543
G D VA IT +Q+D G ++ + AL+ AK+G I + L
Sbjct: 180 YGEADMPVAIMPRLGEITLLQLD---GNLTREEFLEALELAKKGIKRIYQLQREALKSKY 236
Query: 544 LQLGE 548
++ E
Sbjct: 237 GEIAE 241
Score = 55.8 bits (135), Expect = 4e-08
Identities = 52/211 (24%), Positives = 91/211 (43%), Gaps = 17/211 (8%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP----LTVNYQERTYA 69
RP+K+E G + +DG+ +G ++A V R + P L V Y ++
Sbjct: 25 RPIKIEVGVLKN-ADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFS 83
Query: 70 VGKIPGGYLRRESRPTENEILISRMIDRSIRP--LFSKCYKNETQVIINVMQHDLESSPH 127
V + R+ P I IS++I ++ P + + V I V+Q D +
Sbjct: 84 VDE------RKRPGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQAD--AGTR 135
Query: 128 VVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQ-GSLDLFVSGTQDAVL 186
V + AAS AL +G+P V G V ++G VL+ +ED G D+ V+
Sbjct: 136 VAGITAASLALADAGIPMRDLVAGCAVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGE 195
Query: 187 MVELEAN-QLSEDVVLDAIIFGHNECKPVIE 216
+ L+ + L+ + L+A+ K + +
Sbjct: 196 ITLLQLDGNLTREEFLEALELAKKGIKRIYQ 226
>gnl|CDD|131120 TIGR02065, ECX1, archaeal exosome-like complex exonuclease 1. This
family contains the archaeal protein orthologous to the
eukaryotic exosome protein Rrp41. It is somewhat more
distantly related to the bacterial protein ribonuclease
PH. An exosome-like complex has been demonstrated
experimentally for the Archaea in Sulfolobus
solfataricus, so members of this family are designated
exosome complex exonuclease 1, after usage in SwissProt.
Length = 230
Score = 105 bits (263), Expect = 5e-23
Identities = 76/239 (31%), Positives = 118/239 (49%), Gaps = 15/239 (6%)
Query: 307 MLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSL 366
+L+ VR+DGR + +R I + G+L+ GS+ G T+ I V G RE + L
Sbjct: 3 ILEDGVRLDGRKPDELRPIKIEAGVLKNADGSAYVEFGGTKIIAAV-YGPRE--MHPRHL 59
Query: 367 SGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYT-LRI 425
R + Y+ P +T E R G PSRREI ++ R A+ P + QFP T + +
Sbjct: 60 QLPDRAVLRVRYHMAPFSTDERKRPG-PSRREIEISKVIREALEPAI-LLEQFPRTAIDV 117
Query: 426 VSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDH 485
E+ ++D + A + +SLAL DAG+P+ V G+A+G V D ++L D++ +ED
Sbjct: 118 FIEVLQADAGTRCAGLTAASLALADAGIPMRDLVVGVAVGKV---DGVVVL-DLNEEEDM 173
Query: 486 LGHMDFKVAGTDS--GITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSES 542
G D VA IT +Q+D G ++ + AL A +G I + L
Sbjct: 174 YGEADMPVAMMPKLGEITLLQLD---GDMTPDEFRQALDLAVKGIKIIYQIQREALKNK 229
Score = 54.4 bits (131), Expect = 1e-07
Identities = 47/165 (28%), Positives = 79/165 (47%), Gaps = 17/165 (10%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATV-----VYDRSLKDGQDFFPLTVNYQERTY 68
RP+K+E G + + +DG+ +G T ++A V ++ R L+ D L V Y +
Sbjct: 19 RPIKIEAG-VLKNADGSAYVEFGGTKIIAAVYGPREMHPRHLQL-PDRAVLRVRYHMAPF 76
Query: 69 AVGKIPGGYLRRESRPTENEILISRMIDRSIRP--LFSKCYKNETQVIINVMQHDLESSP 126
+ + R+ P+ EI IS++I ++ P L + + V I V+Q D +
Sbjct: 77 STDE------RKRPGPSRREIEISKVIREALEPAILLEQFPRTAIDVFIEVLQAD--AGT 128
Query: 127 HVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQ 171
+ AAS AL +G+P VVG V ++G VL+ +ED
Sbjct: 129 RCAGLTAASLALADAGIPMRDLVVGVAVGKVDGVVVLDLNEEEDM 173
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 84.2 bits (209), Expect = 1e-16
Identities = 40/89 (44%), Positives = 52/89 (58%), Gaps = 5/89 (5%)
Query: 601 AEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKT 660
E A +E + S +V +G V ++ DFGAFV G DGLVHIS+LS ERV K
Sbjct: 177 EERAAKKEELLSSLKEGDV---VEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKP 232
Query: 661 SDVVKEGDTVWVKLLDFD-DRGKIKLSMK 688
S+VV G V VK+L D + +I LS+K
Sbjct: 233 SEVVSVGQEVEVKVLSIDWETERISLSLK 261
Score = 76.5 bits (189), Expect = 2e-14
Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD 678
+ +G V ++ DFGAFV +GLVHISQ+S + +A S+V++EG V VK+L+ +
Sbjct: 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVN 336
Query: 679 -DRGKIKLSMK 688
+ +I LS+K
Sbjct: 337 EEEKRISLSIK 347
Score = 54.5 bits (132), Expect = 8e-08
Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 4/90 (4%)
Query: 606 AREMIRSITDVPEVNK--IYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTERVAKTSD 662
E S+ V EV + G+V+KV D FV+ G + +G++ IS+LS + + +D
Sbjct: 2 MEEFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDIND 61
Query: 663 VVKEGDTVWVKLLDF-DDRGKIKLSMKVVD 691
VVK GD + V +L D G + LS + ++
Sbjct: 62 VVKVGDELEVYVLKVEDGEGNLLLSKRRLE 91
>gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 76.9 bits (190), Expect = 2e-14
Identities = 36/78 (46%), Positives = 50/78 (64%), Gaps = 1/78 (1%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD 678
V I G+VV++ FGAFV DGLVHISQ+S +R+ K DV+ EG+ V K+L+ D
Sbjct: 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVD 621
Query: 679 DRGK-IKLSMKVVDQNTG 695
K I+LS+K V++ G
Sbjct: 622 PEEKRIRLSIKEVEEEPG 639
Score = 75.0 bits (185), Expect = 6e-14
Identities = 33/72 (45%), Positives = 48/72 (66%), Gaps = 2/72 (2%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
E + +G+V ++ DFGAFV G DGL+H+S++S RV K SDV+K GD + V +LD
Sbjct: 476 EEGDVVEGEVKRLTDFGAFVDIGGV-DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDI 534
Query: 678 D-DRGKIKLSMK 688
D + K+ LS+K
Sbjct: 535 DKENKKLSLSLK 546
Score = 46.5 bits (111), Expect = 3e-05
Identities = 33/141 (23%), Positives = 61/141 (43%), Gaps = 16/141 (11%)
Query: 558 IPPDQIRNVIGMGGKVIRG------IVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIR 611
+P + + V +G V G I+E+ K++ ++ + E E +
Sbjct: 244 LPEEWFKGVKIIG--VTAGASTPDWIIEEVIKKMS-------ELDNMEEVEENEQLEYMN 294
Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVW 671
+ I KG VV V + FV +G++ + +L+ + ++ + VK GD +
Sbjct: 295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354
Query: 672 VKLLDF-DDRGKIKLSMKVVD 691
VK+L D+ G + LS K D
Sbjct: 355 VKVLKLEDEDGYVVLSKKEAD 375
>gnl|CDD|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 71.1 bits (175), Expect = 8e-13
Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 1/72 (1%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
EV + +G V ++ FGAFV +GL+ IS+LS +RV +V+K GD V VK+L
Sbjct: 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 678 D-DRGKIKLSMK 688
D ++G+I LS+K
Sbjct: 61 DEEKGRIILSLK 72
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 69.8 bits (172), Expect = 2e-12
Identities = 33/90 (36%), Positives = 53/90 (58%), Gaps = 7/90 (7%)
Query: 601 AEIEAAR-EMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAK 659
E R E++ ++ E ++ +G V + D+GAFV G DGL+HI+ +S +RV
Sbjct: 186 EERAEEREELLENL----EEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNH 240
Query: 660 TSDVVKEGDTVWVKLLDFD-DRGKIKLSMK 688
S+VV GD V VK+L FD ++ ++ L +K
Sbjct: 241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270
Score = 59.8 bits (146), Expect = 2e-09
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLD 676
V KG+V + D+GAFV +GLVH+S++S T++ S VV G V V +L+
Sbjct: 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLE 344
Query: 677 FD-DRGKIKLSMKVVDQN 693
D ++ +I L +K +N
Sbjct: 345 IDEEKRRISLGLKQCKEN 362
Score = 59.4 bits (145), Expect = 3e-09
Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDF 677
V + +G+V + DFGAFV G DGLVH+S +S ++ + ++ K+GD V +L
Sbjct: 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV 432
Query: 678 D-DRGKIKLSMK 688
D ++ +I L +K
Sbjct: 433 DVEKERISLGIK 444
Score = 58.6 bits (143), Expect = 5e-09
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD 678
I G V +V D GAFV +GL+ S+LS +RV ++V+K GD V K+++ D
Sbjct: 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINID 519
Query: 679 -DRGKIKLSMKVVDQ 692
+I LS+K +D+
Sbjct: 520 RKNRRISLSIKALDE 534
>gnl|CDD|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 68.2 bits (167), Expect = 6e-12
Identities = 32/79 (40%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTV 670
++ D + G+VV++ FGAFV +GLVH+S++S T RV K DVV GD V
Sbjct: 285 TVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAV 344
Query: 671 WVKLLDFD-DRGKIKLSMK 688
VK+ D D + +I LS++
Sbjct: 345 AVKIKDIDPAKRRISLSLR 363
Score = 65.1 bits (159), Expect = 6e-11
Identities = 30/72 (41%), Positives = 41/72 (56%), Gaps = 5/72 (6%)
Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681
+ +G V ++ FGAFV +G+VHIS+LS RV K + V GDTV VK+L +
Sbjct: 205 VVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAK 264
Query: 682 K-----IKLSMK 688
K I LS+K
Sbjct: 265 KGKGLRISLSIK 276
Score = 28.5 bits (64), Expect = 5.9
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL--LD 676
G V K FG FV+ GL+ S +S T + +K GD+V + + +D
Sbjct: 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEID 438
Query: 677 FDDRGKIKLS 686
R KI L+
Sbjct: 439 TAKR-KISLA 447
>gnl|CDD|180268 PRK05807, PRK05807, hypothetical protein; Provisional.
Length = 136
Score = 65.2 bits (159), Expect = 6e-11
Identities = 33/83 (39%), Positives = 49/83 (59%), Gaps = 3/83 (3%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
+ I +G VV + +FGAFV G + GLVHIS+++ V + +KE D V VK++
Sbjct: 4 KAGSILEGTVVNITNFGAFVEVEG-KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI 62
Query: 678 DDRGKIKLSMK--VVDQNTGKPI 698
DD GKI LS+K + + + KP
Sbjct: 63 DDNGKISLSIKQAMKQKKSVKPA 85
>gnl|CDD|181215 PRK08059, PRK08059, general stress protein 13; Validated.
Length = 123
Score = 64.3 bits (157), Expect = 1e-10
Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
EV + G+V + +GAFV GLVHIS+++ V D + GD V VK+L
Sbjct: 6 EVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSV 65
Query: 678 D-DRGKIKLSMK 688
D ++GKI LS++
Sbjct: 66 DEEKGKISLSIR 77
>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 63.5 bits (155), Expect = 2e-10
Identities = 31/71 (43%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD 678
+ +I G+V K++ FGAFV +GLVHIS+L+ V VV+ GD V+VK++D D
Sbjct: 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDID 352
Query: 679 -DRGKIKLSMK 688
+R +I LS+K
Sbjct: 353 LERRRISLSLK 363
Score = 62.8 bits (153), Expect = 3e-10
Identities = 34/75 (45%), Positives = 50/75 (66%), Gaps = 7/75 (9%)
Query: 620 NKIYKGQVVK-----VMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
N++ KGQV K +++FGAFV G DGLVH+S+LS + + S+VV+ G V V++
Sbjct: 204 NQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEV 262
Query: 675 LDFD-DRGKIKLSMK 688
LD D DR ++ LS+K
Sbjct: 263 LDVDMDRERVSLSLK 277
>gnl|CDD|162009 TIGR00717, rpsA, ribosomal protein S1. This model provides trusted
hits to most long form (6 repeat) examples of RpsA.
Among homologs with only four repeats are some to which
other (perhaps secondary) functions have been assigned.
Length = 516
Score = 62.8 bits (153), Expect = 3e-10
Identities = 35/92 (38%), Positives = 56/92 (60%), Gaps = 6/92 (6%)
Query: 603 IEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSD 662
+A E++ ++ + V KG V + DFGAFV G DGL+HI+ +S +RV S+
Sbjct: 175 SQAREELLENLKEGDVV----KGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSE 229
Query: 663 VVKEGDTVWVKLLDFD-DRGKIKLSMKVVDQN 693
VK G V VK++ FD ++G+I LS+K + ++
Sbjct: 230 YVKVGQEVKVKVIKFDKEKGRISLSLKQLGED 261
Score = 60.1 bits (146), Expect = 2e-09
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDF 677
V G+V + D+G FV +GLVH+S++S ++ + S VVK+GD V V +LD
Sbjct: 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDI 331
Query: 678 D-DRGKIKLSMKVVDQN 693
D +R ++ L +K N
Sbjct: 332 DPERRRLSLGLKQCKAN 348
Score = 54.7 bits (132), Expect = 8e-08
Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD 678
V + KG+V ++ DFGAFV G +GL+ S+LS R +D +K GD V K++D D
Sbjct: 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDID 505
Query: 679 -DRGKIKLSMK 688
K+ LS+K
Sbjct: 506 KKNRKVSLSVK 516
Score = 47.4 bits (113), Expect = 1e-05
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKE-GDTVWVKLLDF 677
V G++ K+ DFGAFV G DGL+H+S +S ++ + +D + + GD + +L
Sbjct: 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV 418
Query: 678 DDRGK-IKLSMK 688
D K I L +K
Sbjct: 419 DKEKKRISLGVK 430
>gnl|CDD|181488 PRK08582, PRK08582, hypothetical protein; Provisional.
Length = 139
Score = 62.4 bits (152), Expect = 4e-10
Identities = 31/71 (43%), Positives = 45/71 (63%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
EV +G+V + +FGAFV + GLVHIS+++ V +D +K GD V VK+L+
Sbjct: 4 EVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNV 63
Query: 678 DDRGKIKLSMK 688
+D GKI LS+K
Sbjct: 64 EDDGKIGLSIK 74
>gnl|CDD|131021 TIGR01966, RNasePH, ribonuclease PH. This bacterial enzyme,
ribonuclease PH, performs the final 3'-trimming and
modification of tRNA precursors. This model is
restricted absolutely to bacteria. Related families
outside the model include proteins described as probable
exosome complex exonucleases (rRNA processing) and
polyribonucleotide nucleotidyltransferases (mRNA
degradation). The most divergent member within the
family is RNase PH from Deinococcus radiodurans.
Length = 236
Score = 61.2 bits (149), Expect = 9e-10
Identities = 55/208 (26%), Positives = 87/208 (41%), Gaps = 35/208 (16%)
Query: 313 RMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRN 372
R DGR + +R +S L+ GS L G+T+ + ++ +E+ L G+
Sbjct: 1 RPDGRKPDQLRPVSITRDFLKHAEGSVLIEFGNTKVLCTASV----EEKVPPFLRGSGEG 56
Query: 373 DFMMHYNFLPCATGEVSRMGAPSRREIGHG----------RLARRAIHPVLPQTAQFPYT 422
Y LP AT R RRE G RL RA+ V+ A T
Sbjct: 57 WITAEYGMLPRATQT--RN----RRESAKGKQSGRTQEIQRLIGRALRAVVDLEALGERT 110
Query: 423 LRIVSEITESDGSSSMATVCGSSLALMDA-----------GVPISKPVAGIAMGLVKDGD 471
+ I ++ ++DG + A++ G+ +AL DA PI VA +++G+V
Sbjct: 111 IWIDCDVIQADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGE- 169
Query: 472 DFIILSDISGDEDHLGHMDFKVAGTDSG 499
+ D+ +ED +D V T SG
Sbjct: 170 ---PVLDLDYEEDSAADVDMNVVMTGSG 194
Score = 34.3 bits (79), Expect = 0.11
Identities = 52/233 (22%), Positives = 88/233 (37%), Gaps = 42/233 (18%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSL---KDGQDFFPLTVNY------- 63
RP+ + + ++G+VL +G T VL T + + G +T Y
Sbjct: 11 RPVSITRD-FLKHAEGSVLIEFGNTKVLCTASVEEKVPPFLRGSGEGWITAEYGMLPRAT 69
Query: 64 ---QERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVII--NVM 118
R A GK G R E I R+I R++R + E + I +V+
Sbjct: 70 QTRNRRESAKGKQSG-------RTQE----IQRLIGRALRAVVDLEALGERTIWIDCDVI 118
Query: 119 QHDLESSPHVV--SMVAASAAL-------MLSGLPFEGPVVGAQVDYINGQYVLNPRLDE 169
Q D + + + VA + A+ +L P V V ++G+ VL+ +E
Sbjct: 119 QADGGTRTASITGAFVALADAISKLHKRGILKESPIRDFVAAVSVGIVDGEPVLDLDYEE 178
Query: 170 DQGS-LDLFVSGTQDAVLMVEL----EANQLSEDVVLDAIIFGHNECKPVIEA 217
D + +D+ V T VE+ E S D + + + +IE
Sbjct: 179 DSAADVDMNVVMTGSGGF-VEVQGTAEEGPFSRDELNKLLDLAKKGIRELIEL 230
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal
protein S1; Provisional.
Length = 863
Score = 58.6 bits (141), Expect = 5e-09
Identities = 33/82 (40%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDF 677
VN + KG+V K+ DFGAF+ +GL HIS+ S ++ +K SD+VK GD V +L +
Sbjct: 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY 637
Query: 678 D-DRGKIKLSMKVVDQNTGKPI 698
D G++ L +K V N + I
Sbjct: 638 DIQAGRVSLGLKQVTANPWEEI 659
Score = 42.8 bits (100), Expect = 3e-04
Identities = 28/86 (32%), Positives = 44/86 (51%), Gaps = 2/86 (2%)
Query: 604 EAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDV 663
E AR+ + + G V FGAF+ G DGL+H++ +S VA+ +
Sbjct: 478 ERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREF 536
Query: 664 VKEGDTVWVKLLDFDDRGK-IKLSMK 688
VK+G T+ +K++ D K I LS+K
Sbjct: 537 VKKGQTIELKVIRLDQAEKRINLSLK 562
Score = 33.9 bits (77), Expect = 0.15
Identities = 40/178 (22%), Positives = 72/178 (40%), Gaps = 41/178 (23%)
Query: 554 EIMAIPPDQIRNVIGMGGKVIRGIVEQTGAK------------VNIDDDGTVKIASSSLA 601
++ A P ++I +G + R IV+ T A +++DD VK +
Sbjct: 650 QVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADH 709
Query: 602 EIEAAREM-----------------IRSITDVP--------EVNKIYKGQVVKVMDFGAF 636
E+E +E+ ++ ++D P V +G+V V DFG F
Sbjct: 710 ELEVGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIF 769
Query: 637 VHFCGARDGLVHISQLSTERVAKTSDVVKE---GDTVWVKLLDFDDRGKIKLSMKVVD 691
V G +GLV L R + +++ GD V ++D + + + K++ V D
Sbjct: 770 VRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDR-KVAFSVRD 826
>gnl|CDD|179696 PRK03987, PRK03987, translation initiation factor IF-2 subunit
alpha; Validated.
Length = 262
Score = 55.2 bits (134), Expect = 5e-08
Identities = 30/82 (36%), Positives = 48/82 (58%), Gaps = 3/82 (3%)
Query: 615 DVPEVNKIYKGQVVKVMDFGAFVHF--CGARDGLVHISQLSTERVAKTSDVVKEGDTVWV 672
+ PE ++ G V +V DFGAFV ++G +HIS++++ V D VKEG V
Sbjct: 4 EWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVC 63
Query: 673 KLLDFD-DRGKIKLSMKVVDQN 693
K++ D +G I LS+K V+++
Sbjct: 64 KVIRVDPRKGHIDLSLKRVNEH 85
>gnl|CDD|181471 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 53.7 bits (130), Expect = 1e-07
Identities = 29/95 (30%), Positives = 53/95 (55%), Gaps = 18/95 (18%)
Query: 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------K 659
++ PE+ ++ +G+VV+V++FGAFV G DGL+HISQ+ + ++ +
Sbjct: 73 DALVFKPELQEVVEGEVVEVVEFGAFVRI-GPVDGLLHISQIMDDYISYDPKNGRLIGKE 131
Query: 660 TSDVVKEGDTVWVKL--LDFDDRG----KIKLSMK 688
+ V+K GD V ++ + +R KI L+M+
Sbjct: 132 SKRVLKVGDVVRARIVAVSLKERRPRGSKIGLTMR 166
>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain.
Length = 69
Score = 51.9 bits (125), Expect = 5e-07
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDG----TVKIASSSLAEIEA 605
P + IP D++ +IG GG I+ I E+TG K++I +DG V+I + +E
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEI-TGPPENVEK 59
Query: 606 AREMIRSI 613
A E+I I
Sbjct: 60 AAELILEI 67
>gnl|CDD|180908 PRK07252, PRK07252, hypothetical protein; Provisional.
Length = 120
Score = 47.8 bits (114), Expect = 1e-05
Identities = 23/70 (32%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 624 KGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD-RGK 682
KG + + +GAFV GL+HIS++ T + ++K G+ V V+++DFD+ GK
Sbjct: 8 KGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGK 67
Query: 683 IKLSMKVVDQ 692
LS++ +++
Sbjct: 68 ASLSLRTLEE 77
>gnl|CDD|180960 PRK07400, PRK07400, 30S ribosomal protein S1; Reviewed.
Length = 318
Score = 45.6 bits (108), Expect = 5e-05
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677
EV ++ G V + +GAF+ G GL+HIS++S E + V D + V ++D
Sbjct: 195 EVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDL 253
Query: 678 D-DRGKIKLSMKVVDQNTG 695
D +RG+I LS K ++ G
Sbjct: 254 DAERGRISLSTKQLEPEPG 272
>gnl|CDD|184310 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 181
Score = 44.1 bits (105), Expect = 1e-04
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 4/60 (6%)
Query: 558 IPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASSSLA---EIEAAREMIRSI 613
IP D+I +IG G+ + I E+TG K+ ID + G V I + + AR+++++I
Sbjct: 9 IPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAI 68
>gnl|CDD|132704 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 40.2 bits (95), Expect = 0.002
Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 3/59 (5%)
Query: 558 IPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASSSLAEIEA--AREMIRSI 613
IP D+I +IG GG+ + I E+TG K++ID + G VKI + ARE++++I
Sbjct: 4 IPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAI 62
Score = 27.9 bits (63), Expect = 9.9
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 566 VIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIE---AAREMIRSITDVPEVNKI 622
+IG GGK R I E TG +++ TV I + + E ARE I + + +
Sbjct: 103 IIGEGGKTRRIIEELTGVSISVYGK-TVGI----IGDPEQVQIAREAIEMLIEGAPHGTV 157
Query: 623 YK 624
YK
Sbjct: 158 YK 159
>gnl|CDD|179808 PRK04282, PRK04282, exosome complex RNA-binding protein Rrp42;
Provisional.
Length = 271
Score = 40.2 bits (95), Expect = 0.002
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 296 EDIQAKVVRTVMLD---KKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVV 352
++I ++ + +L K R+DGR + R I + G++++ GS+L G+TQ + V
Sbjct: 5 QEIIPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64
Query: 353 TLGTREDEQYVDS 365
L E + D+
Sbjct: 65 KLE--IGEPFPDT 75
Score = 36.8 bits (86), Expect = 0.018
Identities = 64/241 (26%), Positives = 96/241 (39%), Gaps = 74/241 (30%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP-------LTVNYQ-- 64
RP+++ETG I + ++G+ L G T VLA V L+ G+ F P L VN +
Sbjct: 35 RPIEIETGVIKK-AEGSALVKLGNTQVLAGV----KLEIGEPF-PDTPNEGVLIVNAELL 88
Query: 65 ---ERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVI------- 114
T+ G P P EN I ++R++DR IR SK E VI
Sbjct: 89 PLASPTFEPG--P---------PDENAIELARVVDRGIRE--SKAIDLEKLVIEPGKKVW 135
Query: 115 -----INVMQHD--LESSPHVVSMVAASAALM--------------------LSGLPFEG 147
+ V+ HD L + SM+AA AAL+ LP
Sbjct: 136 VVFIDVYVLDHDGNLLDA----SMLAAVAALLNTKVPAVEEGEDGVVDKLGEDFPLPVND 191
Query: 148 PVVGAQVDYINGQYVLNPRLDEDQGSLDLFVSGTQDA----VLMVELEANQLSEDVVLDA 203
V I +++P L+E+ +D ++ T D V + + +E+ V A
Sbjct: 192 KPVTVTFAKIGNYLIVDPTLEEES-VMDARITITTDEDGNIVAIQKSGIGSFTEEEVDKA 250
Query: 204 I 204
I
Sbjct: 251 I 251
>gnl|CDD|162678 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans.
Length = 709
Score = 39.6 bits (93), Expect = 0.003
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 619 VNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTE-----------RVAKTSDVVKE 666
+ + ++G + V FG FV +GLVHIS L + +T V +
Sbjct: 627 IGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRL 686
Query: 667 GDTVWVKLLDFD-DRGKIKLSM 687
GD V V+++ D D GKI +
Sbjct: 687 GDRVKVRVVKADLDTGKIDFEL 708
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and
eukaryotic form. This family seems to be confined to
the archea and eukaryotic taxa and are quite dissimilar
to E.coli rpoE.
Length = 179
Score = 37.5 bits (87), Expect = 0.014
Identities = 31/95 (32%), Positives = 52/95 (54%), Gaps = 18/95 (18%)
Query: 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------K 659
R++ PE+ +I +G+V+++++FGAFV G DGL H+SQ++ + +
Sbjct: 73 RALVFKPELGEIVEGEVIEIVEFGAFVSL-GPFDGLFHVSQVTDDYCYYDPKESALIGKE 131
Query: 660 TSDVVKEGDTVWVKL--LDFDDR----GKIKLSMK 688
T V+ EGD V ++ L DR KI L+M+
Sbjct: 132 TKKVLDEGDKVRARIVALSLKDRRPEGSKIGLTMR 166
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 34.0 bits (79), Expect = 0.15
Identities = 26/121 (21%), Positives = 50/121 (41%), Gaps = 10/121 (8%)
Query: 558 IPPDQIRNVIGMGGKVIRGIVEQTGAKVNI---DDDGTVKIASSSLAEIEAAREMIRSIT 614
+P I VIG GGK I+ I ++ G +++ D++ + +E ++ + I
Sbjct: 487 VPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVTVEETKKHVILIV 546
Query: 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKT-SDVVKEGDTVWVK 673
K F A V +R G + +++ S +AK + EG+ + V+
Sbjct: 547 GPDYAGKTVDVYAGGEYLFTATV----SRKGEIKVAKNSA--IAKELLRAIDEGEDIRVR 600
Query: 674 L 674
Sbjct: 601 P 601
>gnl|CDD|181926 PRK09521, PRK09521, exosome complex RNA-binding protein Csl4;
Provisional.
Length = 189
Score = 33.4 bits (77), Expect = 0.20
Identities = 26/108 (24%), Positives = 40/108 (37%), Gaps = 15/108 (13%)
Query: 587 IDDDGTVKIASSSLAEIEAAREMIRSITD-----VPEVNKIYKGQVVKVMDFGAFVHFCG 641
+D+G V + I+ I I + + I G+VV V + A V
Sbjct: 27 YEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVS 86
Query: 642 AR----------DGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD 679
+HISQ+S V +D K GD V K++ + D
Sbjct: 87 IEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD 134
>gnl|CDD|128453 smart00148, PLCXc, Phospholipase C, catalytic domain (part); domain
X. Phosphoinositide-specific phospholipases C. These
enzymes contain 2 regions (X and Y) which together form
a TIM barrel-like structure containing the active site
residues. Phospholipase C enzymes (PI-PLC) act as signal
transducers that generate two second messengers,
inositol-1,4,5-trisphosphate and diacylglycerol. The
bacterial enzyme [6] appears to be a homologue of the
mammalian PLCs.
Length = 135
Score = 33.0 bits (76), Expect = 0.24
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 214 VIEAISKLAKMCAKEPIVIDSKDFSKLEEE--MSQMIKE 250
V+EAI A + + P+++ ++ +++ M+QM KE
Sbjct: 74 VLEAIKDFAFVTSPYPVILSLENHCSPDQQAKMAQMFKE 112
>gnl|CDD|181804 PRK09369, PRK09369, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Validated.
Length = 417
Score = 31.9 bits (74), Expect = 0.62
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 572 KVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSI 613
+ + ++ GAKV D +GTV I +S++ EA E+++ +
Sbjct: 51 RTMIELLRSLGAKVEFDGNGTVTIDASNINNTEAPYELVKKM 92
>gnl|CDD|185526 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 31.6 bits (72), Expect = 0.69
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARD--GLVHISQLSTERVAKTSDVVKEGDTVWVKL 674
PE + + +VV++ + GA+V D G++ +S+LS R+ + +++ G V +
Sbjct: 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVV 74
Query: 675 LDFD-DRGKIKLSMKVV 690
L D ++G I LS K V
Sbjct: 75 LRVDKEKGYIDLSKKRV 91
>gnl|CDD|179011 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed.
Length = 638
Score = 29.7 bits (68), Expect = 2.4
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 232 IDSKDFSKLEEEMSQMIKEDLRVS 255
+D +E+EM ++IKE+ +
Sbjct: 112 FTPEDLEAIEKEMKEIIKENYPIE 135
>gnl|CDD|148965 pfam07651, ANTH, ANTH domain. AP180 is an endocytotic accessory
proteins that has been implicated in the formation of
clathrin-coated pits. The domain is involved in
phosphatidylinositol 4,5-bisphosphate binding and is a
universal adaptor for nucleation of clathrin coats.
Length = 276
Score = 30.0 bits (68), Expect = 2.5
Identities = 24/126 (19%), Positives = 49/126 (38%), Gaps = 17/126 (13%)
Query: 163 LNPRLDE------DQGSLDLFVSGTQDAVLMVELEANQLSEDV-VLDAIIFGHNECKPVI 215
L+ RLD D G+ + G+ D + L + + L ++ +CKP
Sbjct: 116 LDERLDFHRKLPRDPGTFERVEYGSGDPNERYTMSMEDLLDIIPKLQKLLDRLLKCKPTG 175
Query: 216 EAISKLAKMCAKEPIVIDSKDF--------SKLEEEMSQMIKEDLRVSCFIPEKYVRCKQ 267
A++ + A ++ +S L + ++ K D + I +++V Q
Sbjct: 176 NALTNECIIAALILLIKESFGLYGAINEGIINLLSKFFELSKPDADAALGIYKRFV--SQ 233
Query: 268 IDDLKK 273
+ LK+
Sbjct: 234 FERLKE 239
>gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases.
Length = 654
Score = 29.7 bits (67), Expect = 2.7
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 618 EVNKIYKGQVVKVMDFGAFVHF--CGARDGLVHIS-------QLSTERVA----KTSDVV 664
+V + G++ V FG FV G DGL+HIS E++A T V
Sbjct: 571 KVGTEFSGEISSVTRFGMFVRLDDNGI-DGLIHISTLHNDYYVFDQEKMALIGKGTGKVY 629
Query: 665 KEGDTVWVKLLDFD 678
+ GD V VKL + +
Sbjct: 630 RIGDRVTVKLTEVN 643
>gnl|CDD|181474 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 29.1 bits (66), Expect = 4.3
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 145 FEGPVVGAQVDYINGQYVL---NPRLDEDQ 171
+ GP++G D+I+G Y+L + +++
Sbjct: 492 YGGPIIGGIQDHISGAYLLTRKSTLFTKEE 521
>gnl|CDD|163224 TIGR03347, VI_chp_1, type VI secretion protein, VC_A0111 family.
Work by Mougous, et al. (2006), describes IAHP-related
loci as a type VI secretion system (PubMed:16763151).
This protein family is associated with type VI secretion
loci, although not treated explicitly by Mougous, et al.
Length = 300
Score = 28.3 bits (64), Expect = 6.1
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 2 FDVH-TVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60
F V TVE E+ GR + + + G A G VL + V+DR K PL
Sbjct: 183 FGVPVTVE-EFVGRWVPIPPE--QQSRLGGRNARLGRDAVLGSRVWDRQGKFRLVIGPLD 239
>gnl|CDD|178914 PRK00173, rph, ribonuclease PH; Reviewed.
Length = 238
Score = 28.2 bits (64), Expect = 7.2
Identities = 30/102 (29%), Positives = 44/102 (43%), Gaps = 29/102 (28%)
Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYD----RSLKD-GQDFFPLTVNY----- 63
RP+ + + ++G+VL +G+T VL T + R LK GQ + +T Y
Sbjct: 12 RPVTITRNFT-KHAEGSVLVEFGDTKVLCTASVEEGVPRFLKGQGQGW--VTAEYGMLPR 68
Query: 64 -----QERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIR 100
+R A GK G R E I R+I RS+R
Sbjct: 69 ATHTRNDREAAKGKQGG-------RTQE----IQRLIGRSLR 99
>gnl|CDD|172295 PRK13757, PRK13757, chloramphenicol acetyltransferase; Provisional.
Length = 219
Score = 28.3 bits (63), Expect = 7.7
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 271 LKKKMVSYFSSEHSSWNEGEIVSVFE-DIQAKVVRTVMLD 309
++KK+ Y + + S W+ E F+ Q +TV LD
Sbjct: 1 MEKKITGYTTVDISQWHRKEHFEAFQSVAQCTYNQTVQLD 40
>gnl|CDD|178541 PLN02955, PLN02955, 8-amino-7-oxononanoate synthase.
Length = 476
Score = 28.1 bits (62), Expect = 9.0
Identities = 24/98 (24%), Positives = 50/98 (51%), Gaps = 2/98 (2%)
Query: 128 VVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNP-RLDEDQGSLDLFVSGTQDAVL 186
+V++ + ++ L SG P + V D +N +++ RL E QG++++FV D
Sbjct: 179 MVAIGSVASLLAASGKPLKNEKVAIFSDALNHASIIDGVRLAERQGNVEVFVYRHCDMYH 238
Query: 187 MVELEAN-QLSEDVVLDAIIFGHNECKPVIEAISKLAK 223
+ L ++ ++ VV+ +F + +E +S+L K
Sbjct: 239 LNSLLSSCKMKRKVVVTDSLFSMDGDFAPMEELSQLRK 276
>gnl|CDD|162518 TIGR01753, flav_short, flavodoxin, short chain. Flavodoxins are
small redox-active proteins with a flavin mononucleotide
(FMN) prosthetic group. They can act in nitrogen
fixation by nitrogenase, in sulfite reduction, and
light-dependent NADP+ reduction in during
photosynthesis, among other roles. This model describes
the short chain type. Many of these are involved in
sulfite reduction.
Length = 140
Score = 27.7 bits (62), Expect = 9.5
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 231 VIDSKDFSKLEEEMSQMIKEDLRVSCFIP--EKYVRCKQIDDLKKKMVSY 278
++ DF EE+ + +V+ F Y C+ +DD ++++
Sbjct: 60 DLEQDDFEPFFEELEDIDLGGKKVALFGSGDWGYEFCEAVDDWEERLKEA 109
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.135 0.380
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 11,364,766
Number of extensions: 761175
Number of successful extensions: 1784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1726
Number of HSP's successfully gapped: 80
Length of query: 699
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 599
Effective length of database: 3,833,673
Effective search space: 2296370127
Effective search space used: 2296370127
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.1 bits)