RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780788|ref|YP_003065201.1| transcription elongation
factor NusA [Candidatus Liberibacter asiaticus str. psy62]
(526 letters)
>gnl|CDD|181696 PRK09202, nusA, transcription elongation factor NusA; Validated.
Length = 470
Score = 628 bits (1622), Expect = e-180
Identities = 259/473 (54%), Positives = 356/473 (75%), Gaps = 5/473 (1%)
Query: 5 NRLELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFR 64
ELL+ +AVA EK IDR+VV+ + +++ A + YG ++IRVEI+ +TGDI +FR
Sbjct: 1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFR 60
Query: 65 LLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVRE 124
EVVEEVE+ T +ISL+ AR DP ++G + + + +DFGR+A Q+AKQVI+QK+RE
Sbjct: 61 RWEVVEEVEDPTKEISLEEARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIRE 120
Query: 125 AERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKS 184
AER+R Y E+KD+VGEII+G VKRVE GN+IVDLG ++ ++ R E I REN RPGDRV++
Sbjct: 121 AERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPRENFRPGDRVRA 180
Query: 185 YIYDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSS 244
Y+Y+VR+E RGPQ++LSRTHP+F+ KLF EVPEI +G++++KA++RDPGSRAK+AV S+
Sbjct: 181 YVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSN 240
Query: 245 DSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDED 304
D IDPVGACVGMRGSR+QA+ EL EKIDI++WS D A F+INAL PA V+ VV+DED
Sbjct: 241 DPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDED 300
Query: 305 VGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDFNERTQFFMQ 364
+V+VP +QLSLAIG+ GQNVRLAS+LTGW IDI+TEEE S RQ +F+ FM+
Sbjct: 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFME 360
Query: 365 AINVDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYLEGIDITL 424
A+++DE IA LLV EGF+ +EELA V + E+ IEGFDEET E++ RA+E LE +
Sbjct: 361 ALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDEETVEELRERAKEALETEALAQ 420
Query: 425 QKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWSENK 477
++K+ +++L S+ G+D ++ L E GIKT+EDLA +VD+L+ ++
Sbjct: 421 EEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDE 468
>gnl|CDD|162623 TIGR01953, NusA, transcription termination factor NusA. This model
describes NusA, or N utilization substance protein A, a
bacterial transcription termination factor. It binds to
RNA polymerase alpha subunit and promotes termination at
certain RNA hairpin structures. It is named for the
interaction in E. coli of phage lambda antitermination
protein N with the N-utilization substance, consisting
of NusA, NusB, NusE (ribosomal protein S10), and nusG.
This model represents a region of NusA shared in all
bacterial forms, and including an S1 (pfam00575) and a
KH (pfam00013) RNA binding domains. Proteobacterial
forms have an additional C-terminal region, not included
in this model, with two repeats of 50-residue domain
rich in acidic amino acids.
Length = 341
Score = 438 bits (1128), Expect = e-123
Identities = 179/341 (52%), Positives = 252/341 (73%), Gaps = 2/341 (0%)
Query: 8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLE 67
E L +A+A EK I + V+ + +++++A + +G ++ V I+ +TGDI+++R E
Sbjct: 1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKE 60
Query: 68 VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAER 127
VVEEVE+ + +ISL+ AR+ DP + IG V +PP +FGR+A Q+AKQVI+QK+REAER
Sbjct: 61 VVEEVEDPSLEISLEDAREIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAER 120
Query: 128 DRQYLEFKDKVGEIISGTVKRVEY-GNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYI 186
+R Y EF K GEIISGTVKRV GN+ V+LG ++G++ + E I E R GDR+K+Y+
Sbjct: 121 ERVYDEFSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPGEKFRIGDRIKAYV 180
Query: 187 YDVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDS 246
Y+VR+ +GPQ++LSRTHP+F+ +L +EVPEI +GI+++K ++R+PG R K+AV S+D
Sbjct: 181 YEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDE 240
Query: 247 SIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDV 305
+IDPVGACVG +GSR+QA+ EL EKIDI+ +S D A F+ NAL PA V V VLDED
Sbjct: 241 NIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVEVLDEDK 300
Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346
EV+VP +QLSLAIG+ GQNVRLAS+LTGW ID+ TE +
Sbjct: 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTESQ 341
>gnl|CDD|183442 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 385 bits (992), Expect = e-107
Identities = 150/340 (44%), Positives = 229/340 (67%), Gaps = 1/340 (0%)
Query: 8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLE 67
E L+ A+ EK I ++ ++ + ++ A + YG ++RV+ + +TG++ ++ + E
Sbjct: 4 EDLEALRALEEEKGISKEDLIEAIEAALLSAYKRNYGQAQNVRVDFDRKTGEVKVYAVKE 63
Query: 68 VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAER 127
VV+EV + +ISL+ A +P+ ++G V+ + P DFGR+A Q+AKQVI+Q++REAER
Sbjct: 64 VVDEVFDSRLEISLEDALAINPAYELGDVIEIEVTPKDFGRIAAQTAKQVIMQRLREAER 123
Query: 128 DRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPGDRVKSYIY 187
+ Y EF ++ G+I++G V+R + V V+LG + V+ E I E + GDR+K Y+
Sbjct: 124 EIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIPGETYKHGDRIKVYVV 183
Query: 188 DVRREQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSS 247
V + +GPQ+ +SRTHP + +LF +EVPEIY+G V++K+++R+ G R K+AV S++ +
Sbjct: 184 KVEKTTKGPQIFVSRTHPGLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPN 243
Query: 248 IDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDVG 306
+D GACVG +G RVQ +V+EL+ EKIDI+ WS D A FV NAL PA V V V DE+
Sbjct: 244 VDAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFVANALSPAKVVSVEVDDEEEK 303
Query: 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEE 346
V+VP QLSLAIG+ GQN RLA++LTGW IDI +E E
Sbjct: 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSESE 343
>gnl|CDD|183443 PRK12328, nusA, transcription elongation factor NusA; Provisional.
Length = 374
Score = 230 bits (589), Expect = 7e-61
Identities = 120/362 (33%), Positives = 201/362 (55%), Gaps = 19/362 (5%)
Query: 9 LLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLEV 68
+ I +++AYEK + ++V + +++ K A+ G + VEI+PE + L++ +EV
Sbjct: 4 ISDIIESIAYEKGLPIEMVKEAVKEALIKTAKKELGPEYEYDVEIDPENKTLKLYQKIEV 63
Query: 69 V--------EEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVI-- 118
V + E + ISL A++ DPS++IG ++ L + GR A + + +
Sbjct: 64 VADDDERLQNDPEKF---ISLSEAKEIDPSVEIGDELTYELSLENMGRTAANTLFKELEY 120
Query: 119 -IQKVREAERDRQYLEFKDKVGEIISGTVKRVEY-GNVIVDLGNSDGVIRRDETISRENL 176
IQ++ E + + ++K KVG+I+ GTV RV+ N +++ V+ I E
Sbjct: 121 HIQRLLE---ESIFEKYKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKGEKF 177
Query: 177 RPGDRVKSYIYDVRRE-QRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVSRDPGS 235
+ GD VK+ + V+ + G + LSRT P+F+ L +EVPEI +G V + +R PG
Sbjct: 178 KVGDVVKAVLKRVKIDKNNGILIELSRTSPKFLEALLELEVPEIKDGEVIIIHSARIPGE 237
Query: 236 RAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAI 295
RAK+A+FS++ +IDP+GA VG++G R+ AV EL E ID + +S F+ AL PAI
Sbjct: 238 RAKVALFSNNPNIDPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIFIARALAPAI 297
Query: 296 VTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKDF 355
++ V ++E+ + V + +Q S AIG+ G N+RLAS LTG+ I++ +
Sbjct: 298 ISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSKENASNESE 357
Query: 356 NE 357
E
Sbjct: 358 KE 359
>gnl|CDD|183444 PRK12329, nusA, transcription elongation factor NusA; Provisional.
Length = 449
Score = 221 bits (564), Expect = 5e-58
Identities = 128/299 (42%), Positives = 180/299 (60%), Gaps = 20/299 (6%)
Query: 63 FRLLE---VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPP--MDFGRVAVQSAKQV 117
FR+L +VEEVEN QISL + +G V + P DFGR+A KQV
Sbjct: 72 FRVLATKIIVEEVENEDHQISLAEVQQVADEAQLGDTVVLDVTPEQEDFGRMAAIQTKQV 131
Query: 118 IIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDG------VIRRDETI 171
+ QK+R+ +R EF+D +++ V R E +VI+ + + G + + E +
Sbjct: 132 LAQKLRDQQRKMIQEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL 191
Query: 172 SRENLRPGDRVKSYIYDVRR-EQRGPQVLLSRTHPQFMVKLFHMEVPEIYNGIVQVKAVS 230
+N R K ++ +V +RGPQ+ +SR + +V LF EVPEI G+V++ AV+
Sbjct: 192 PNDNYRANATFKVFLKEVSEGPRRGPQLFVSRANAGLVVYLFENEVPEIEEGVVRIVAVA 251
Query: 231 RDP-------GSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEKIDIVVWSPDS 283
R+ G R K+AV + + +DPVGAC+G RGSR+QAVV ELR EKID++ WSPD
Sbjct: 252 REANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP 311
Query: 284 ATFVINALRPAIVTKVVLDEDVGRI-EVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341
AT++ NAL PA V +V L + GR V+VP +QLSLAIG+ GQNVRLA++LTGW IDI
Sbjct: 312 ATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDI 370
>gnl|CDD|149546 pfam08529, NusA_N, NusA N-terminal domain. This domain represents
the RNA polymerase binding domain of NusA.
Length = 122
Score = 156 bits (398), Expect = 1e-38
Identities = 59/122 (48%), Positives = 89/122 (72%)
Query: 8 ELLQIADAVAYEKSIDRDVVLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLFRLLE 67
ELL+ DA+A EK ID++V++ + +++ A + YG ++RVEI+ ETG+I ++R E
Sbjct: 1 ELLEAIDAIAREKGIDKEVLIEAIEEALLSAYKKKYGEDENVRVEIDRETGEIEVYRRKE 60
Query: 68 VVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAER 127
VVEEVE+ +ISL+ A++ DP +IG + + + P DFGR+A Q+AKQVIIQK+REAER
Sbjct: 61 VVEEVEDPDTEISLEEAKEIDPDAEIGDEIEEEVTPKDFGRIAAQTAKQVIIQKIREAER 120
Query: 128 DR 129
+R
Sbjct: 121 ER 122
>gnl|CDD|131009 TIGR01954, nusA_Cterm_rpt, transcription termination factor NusA,
C-terminal duplication. NusA is a bacterial
transcription termination factor. It is named for its
interaction with phage lambda protein N, as part of the
N utilization substance. Some members of the NusA family
have a long C-terminal extension. This model represents
an acidic 50-residue region found in two copies toward
the C-terminus of most Proteobacterial NusA proteins,
spaced about 26 residues apart. Analogous C-terminal
extensions in some other bacterial lineages lack
apparent homology but appear similarly acidic.
Length = 50
Score = 64.2 bits (157), Expect = 7e-11
Identities = 32/50 (64%), Positives = 36/50 (72%)
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417
+DE IA LLV EGF VE+LA V I E+ SIEGFDEETA E+ RAR L
Sbjct: 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
>gnl|CDD|162622 TIGR01952, nusA_arch, NusA family KH domain protein, archaeal.
This model represents a family of archaeal proteins
found in a single copy per genome. It contains two KH
domains (pfam00013) and is most closely related to the
central region bacterial NusA, a transcription
termination factor named for its iteraction with phage
lambda protein N in E. coli. The proteins required for
antitermination by N include NusA, NusB, nusE (ribosomal
protein S10), and nusG. This system, on the whole,
appears not to be present in the Archaea.
Length = 141
Score = 45.1 bits (107), Expect = 4e-05
Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 251 VGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKVVLDEDVGRIEV 310
+GA +G G V+ + EL + I+++ +S + FV N L PA V V + E G+
Sbjct: 44 MGAAIGKGGENVKRL-EELIGKSIELIEYSENLEEFVANKLAPAEVKNVTVSEFNGKKVA 102
Query: 311 I--VPKEQLSLAIGRRGQNVRLASQLTGWTIDI 341
V +AIG+ G+N+ A +L DI
Sbjct: 103 YVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135
Score = 32.4 bits (74), Expect = 0.29
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 301 LDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347
L +D R+ +V + ++ AIG+ G+NV+ +L G +I++I E+
Sbjct: 28 LIDDRNRVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN 74
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 44.4 bits (106), Expect = 6e-05
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 3/86 (3%)
Query: 251 VGACVGMRGSRVQAVVTELRDEKIDIVVWSPDSATFVINALRPAIVTKV-VLDEDVGRIE 309
+G +G G V+ + E + I++V +S D F+ N PA V V + ++ ++
Sbjct: 43 MGLAIGKGGENVKRL-EEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIKKKNGDKVA 101
Query: 310 VI-VPKEQLSLAIGRRGQNVRLASQL 334
+ V E +AIG+ G+N+ A L
Sbjct: 102 YVEVAPEDKGIAIGKNGKNIERAKDL 127
Score = 37.5 bits (88), Expect = 0.008
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 294 AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347
A V ++D+D RI +V + + LAIG+ G+NV+ + G I+++ +D
Sbjct: 22 ATVKDCIIDDD--RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD 73
>gnl|CDD|178853 PRK00087, PRK00087, 4-hydroxy-3-methylbut-2-enyl diphosphate
reductase/S1 RNA-binding domain protein; Reviewed.
Length = 647
Score = 41.1 bits (97), Expect = 6e-04
Identities = 28/99 (28%), Positives = 52/99 (52%), Gaps = 13/99 (13%)
Query: 111 VQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVIRRDET 170
V S K I+++ +E +++ + + G+++ G VKR+ VD+G DG++ E
Sbjct: 453 VLSRK-AILEEEKEKKKEETWNSLE--EGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSE- 508
Query: 171 IS-------RENLRPGDRVKSYIYDVRREQRGPQVLLSR 202
IS + L+ GD +K YI D+ +E + ++ LS
Sbjct: 509 ISWGRVEKPSDVLKVGDEIKVYILDIDKENK--KLSLSL 545
Score = 33.0 bits (76), Expect = 0.17
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 131 YLEFKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRP------GDRVK 183
LE + + G+I+ GTV V V VD+G S+GVI E E GD ++
Sbjct: 295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354
Query: 184 SYIYDVRREQRGPQVLLSR 202
+ ++ E V+LS+
Sbjct: 355 VKV--LKLEDEDGYVVLSK 371
>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain.
Length = 69
Score = 40.4 bits (95), Expect = 0.001
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 307 RIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDS 348
IEV++P +++ L IG+ G ++ + TG IDI + +
Sbjct: 4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEE 45
>gnl|CDD|128611 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 40.3 bits (95), Expect = 0.001
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 9/73 (12%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGN-SDGVI------RRDETISRENLRPGDRVKSYIYDV 189
+VG+++ GTV + VDLGN +G+I + E L+ GD VK + V
Sbjct: 1 EVGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV 60
Query: 190 RREQRGPQVLLSR 202
E+ +++LS
Sbjct: 61 DEEKG--RIILSL 71
>gnl|CDD|180520 PRK06299, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 565
Score = 40.1 bits (95), Expect = 0.001
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISREN----LRPGDRVKSYIYDVRR 191
+ G I+ GTV ++ V+VD+G S+G I +E E ++ GD V+ Y+ R
Sbjct: 29 REGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEE-FKNEQGELEVKVGDEVEVYV--ERI 85
Query: 192 EQRGPQVLLSR 202
E + +LSR
Sbjct: 86 EDGFGETVLSR 96
Score = 32.4 bits (75), Expect = 0.30
Identities = 25/86 (29%), Positives = 45/86 (52%), Gaps = 12/86 (13%)
Query: 117 VIIQKVREAERDRQYLEFKDKVGEIISGTVKRV-EYGNVIVDLGNSDGVIRRDETIS--- 172
++++ R ER+ + LE + G+++ G VK + +YG VDLG DG++ + IS
Sbjct: 182 AVLEEERAEERE-ELLE-NLEEGQVVEGVVKNITDYG-AFVDLGGVDGLLHITD-ISWKR 237
Query: 173 ----RENLRPGDRVKSYIYDVRREQR 194
E + GD VK + +E++
Sbjct: 238 VNHPSEVVNVGDEVKVKVLKFDKEKK 263
Score = 32.1 bits (74), Expect = 0.34
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 9/66 (13%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISR-------ENLRPGDRVKSYIYD 188
K G I++GTV V+ V+L +G+IR E +SR E L+ GD V++ + +
Sbjct: 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASE-LSRDRVEDATEVLKVGDEVEAKVIN 517
Query: 189 VRREQR 194
+ R+ R
Sbjct: 518 IDRKNR 523
>gnl|CDD|132714 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 36.8 bits (86), Expect = 0.014
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 280 SPDSATFVINALRP--AIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQNVRLASQLTGW 337
P+ A I + P A +T + D+ G EVI+ E+ L IG+ G +R + TGW
Sbjct: 67 PPEEAIEKIKEIVPEEAGITDIYFDDVTG--EVIIEAEKPGLVIGKGGSTLREITAETGW 124
Query: 338 T 338
T
Sbjct: 125 T 125
>gnl|CDD|180655 PRK06676, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 390
Score = 35.6 bits (83), Expect = 0.036
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 10/80 (12%)
Query: 122 VREAERDRQYLEFKD--KVGEIISGTVKRVEYGNVIVDLGNSDGVI-------RRDETIS 172
V E ER + E K G+++ GTV R+ VD+G DG++ R E S
Sbjct: 174 VVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPS 233
Query: 173 RENLRPGDRVKSYIYDVRRE 192
E + G V+ + + E
Sbjct: 234 -EVVSVGQEVEVKVLSIDWE 252
Score = 32.9 bits (76), Expect = 0.20
Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLGNS--DGVIRRDETISRENLRPGDRVKS----YIYDVR 190
+VG++++G V +VE V V++ +GVI E + D VK +Y ++
Sbjct: 16 EVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLK 75
Query: 191 REQRGPQVLLSR 202
E +LLS+
Sbjct: 76 VEDGEGNLLLSK 87
Score = 29.8 bits (68), Expect = 1.7
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 124 EAERDRQYLEFKDKVGEIISGTVKRVEYGNVIVDLGNSDGVI 165
EAE+ LE K + GE++ V V G ++VD+ G I
Sbjct: 91 EAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFI 132
>gnl|CDD|179814 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 34.9 bits (81), Expect = 0.057
Identities = 16/50 (32%), Positives = 21/50 (42%)
Query: 368 VDEIIAHLLVAEGFADVEELACVKISEIASIEGFDEETAVEIQGRAREYL 417
V A L G+ VE +A E++ G E TA +I ARE
Sbjct: 14 VGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAA 63
>gnl|CDD|172339 PRK13806, rpsA, 30S ribosomal protein S1; Provisional.
Length = 491
Score = 33.5 bits (77), Expect = 0.14
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 137 KVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRE---NLRPGDRVKSYIYDVRRE 192
+VG+ I+GTV + +V VD G DGV+ R E + + + GD V+ Y+ V
Sbjct: 33 RVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADGELTVAVGDEVELYVVSV--- 89
Query: 193 QRGPQVLLSR 202
G ++ LS+
Sbjct: 90 -NGQEIRLSK 98
>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 = 32.4 bits (74), Expect = 0.33
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 139 GEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETIS-RENLRPGDRVKSYIYDVRREQRGP 196
G I+ GTV + V VD+G S+G I ++E + ++ GD V+ Y+ R E R
Sbjct: 19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQVGDEVEVYL--DRVEDRFG 76
Query: 197 QVLLSRTHPQ 206
+ +LSR Q
Sbjct: 77 ETVLSREKAQ 86
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 30.2 bits (69), Expect = 1.4
Identities = 10/49 (20%), Positives = 24/49 (48%)
Query: 306 GRIEVIVPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEEDSINRQKD 354
+ V VP++ + IG+ G+ ++ + G ID+ +E+ ++
Sbjct: 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEE 529
>gnl|CDD|162484 TIGR01684, viral_ppase, viral phosphatase. These proteins also
include an N-terminal domain (ca. 125 aas) that is
unique to this clade.
Length = 301
Score = 29.0 bits (65), Expect = 3.3
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 12/86 (13%)
Query: 211 LFHMEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGAC--VGMRGSRVQAVVTE 268
E+ + V P + VF DS++ + V +R R+ +TE
Sbjct: 108 FELEEIYNLNLPSK----VFEPP----HVVVFDLDSTL--ITDEEPVRIRDPRIYDSLTE 157
Query: 269 LRDEKIDIVVWSPDSATFVINALRPA 294
L+ +V+WS V+ ++R
Sbjct: 158 LKKRGCILVLWSYGDRDHVVESMRKV 183
>gnl|CDD|179950 PRK05166, PRK05166, histidinol-phosphate aminotransferase;
Provisional.
Length = 371
Score = 28.9 bits (65), Expect = 3.4
Identities = 39/154 (25%), Positives = 61/154 (39%), Gaps = 36/154 (23%)
Query: 158 LGN-SDGVIRRDETISRENLRPGDRVKSYIYDVRREQRGPQVLLSRTHPQFM---VKLFH 213
LGN S+ +I I R LRPGDRV + P L +P M V+
Sbjct: 93 LGNGSEDLIA---VICRAVLRPGDRVVT--------LY-PSFPLHEDYPTMMGARVERVT 140
Query: 214 MEVPEIYNGIVQVKAVSRDPGSRAKLAVFSSDSSIDPVGACVGMRGSRVQAVVTELRDEK 273
+ ++ AV+R P ++ +FS+ S +PVG+ + ++ V+ E
Sbjct: 141 VTPDLGFDLDALCAAVARAP----RMLMFSNPS--NPVGSW--LTADQLARVLDATPPET 192
Query: 274 IDIVV----WS-------PDSATFVINALRPAIV 296
+ IVV P + T + P IV
Sbjct: 193 L-IVVDEAYAEYAAGDDYPSALTLLKARGLPWIV 225
>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 = 28.6 bits (65), Expect = 4.2
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 307 RIEVI-VPKEQLSLAIGRRGQNVRLASQLTGWTIDIITEEED 347
RIE I + +++ IG G+ +R ++ TG IDI E+D
Sbjct: 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDI---EDD 589
Score = 27.8 bits (63), Expect = 6.2
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 12/57 (21%)
Query: 110 AVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISGTVKR-VEYGNVIVDLGNSDGVI 165
A ++A ++I E E VG+I G V R +++G + L DG++
Sbjct: 601 AAEAAIKMIEGITAEPE-----------VGKIYEGKVVRIMDFGAFVEILPGKDGLV 646
>gnl|CDD|163289 TIGR03491, TIGR03491, RecB family nuclease, putative, TM0106
family. Members of this uncharacterized protein family
are found broadly but sporadically among bacteria. The
N-terminal region is homologous to the Cas4 protein of
CRISPR systems, although this protein family shows no
signs of association with CRISPR repeats.
Length = 457
Score = 28.4 bits (64), Expect = 4.4
Identities = 14/31 (45%), Positives = 17/31 (54%)
Query: 440 IPGIDSKIKVALGENGIKTMEDLAGCSVDDL 470
+PGI L E GI T+EDLA +DL
Sbjct: 212 VPGIGPSRYRLLQELGIHTLEDLAAADPNDL 242
>gnl|CDD|185451 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein;
Provisional.
Length = 1388
Score = 28.5 bits (64), Expect = 4.8
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 32 ADSIQKAARSLYGTMSDIRVEINPETGDISLF 63
AD+ + M+ I+V I+ E G+IS++
Sbjct: 70 ADNKARDKGG--HRMTYIKVTIDEENGEISVY 99
>gnl|CDD|162403 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground.
Length = 1464
Score = 28.3 bits (63), Expect = 5.6
Identities = 21/97 (21%), Positives = 34/97 (35%), Gaps = 19/97 (19%)
Query: 87 RDPSIDIGGVVSDPLPPMDFGRVAVQSAKQVIIQKVREAERDRQYLEFKDKVGEIISG-- 144
D ID + LPP+ V+ + + E +R E+ + +I+G
Sbjct: 729 SDNDIDWDP---NGLPPVVIN--------GVLEEVIFEYALERVQEEWGREDPNVINGIK 777
Query: 145 --TVKRVEYGNVIVDLGNSDGVIRRDETISRENLRPG 179
+ E+ +DL S D I N PG
Sbjct: 778 GIPTELREH----IDLSYSTSFKISDGEIELPNFPPG 810
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 27.9 bits (62), Expect = 6.3
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 13/78 (16%)
Query: 414 REYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGW 473
R LE ++I +++ IRE + +L IP + L + G KT++D+A S +
Sbjct: 593 RRKLEILNIRIKEGIREDLI--DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPE----- 645
Query: 474 SENKGGNIEKFDGFLSSL 491
I+K GF +L
Sbjct: 646 ------RIKKIYGFSDTL 657
>gnl|CDD|182136 PRK09902, PRK09902, hypothetical protein; Provisional.
Length = 216
Score = 27.7 bits (61), Expect = 7.0
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 292 RPAIVTKVVLDEDVGRIEVIVPKEQLSLAIGRRGQ 326
RP IV +V + +++ R VIVPK A+ G+
Sbjct: 63 RPTIVREVAVIKELERAGVIVPKIVFGEAVKIEGE 97
>gnl|CDD|179415 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 27.6 bits (62), Expect = 7.1
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 9/78 (11%)
Query: 404 ETAVEIQGRAREYLEGIDITLQKKIREL------GVSEEL---CSIPGIDSKIKVALGEN 454
ETA + A +D+ L + REL GV EEL + G+ L
Sbjct: 612 ETAEWLLHAAERLASELDLDLARAARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNA 671
Query: 455 GIKTMEDLAGCSVDDLLG 472
GI++ DL +L
Sbjct: 672 GIESRADLRAADKSVVLA 689
>gnl|CDD|151443 pfam10996, Beta-Casp, Beta-Casp domain. The beta-CASP domain is
found C terminal to the beta-lactamase domain in
pre-mRNA 3'-end-processing endonuclease. The active site
of this enzyme is located at the interface of these two
domains.
Length = 124
Score = 27.6 bits (62), Expect = 7.5
Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 16/106 (15%)
Query: 7 LELLQIADAVAYEKSIDRDV---VLSVMADSIQKAARSLYGTMSDIRVEINPETGDISLF 63
ELL I + + E I +DV + S MA + RS + D E D F
Sbjct: 2 QELLLILEELWEEGEIPKDVPIYLDSPMAIKATEIYRSYPEWLRD---EAKEFLLDGFPF 58
Query: 64 RLLEVVEEVENYTCQISLKVARDRDPSIDIGGVVSDPLPPMDFGRV 109
+ L+ V+ VE S ++ R P + +++ + GR
Sbjct: 59 KNLKFVKSVEE-----SRELNRLGGPKV----IIASS-GMLTGGRS 94
>gnl|CDD|179341 PRK01839, PRK01839, Maf-like protein; Reviewed.
Length = 209
Score = 27.8 bits (62), Expect = 8.1
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 395 IASIEGFDEETAVEIQGRAREYLEGID 421
+AS E F + A IQGRA E++E ID
Sbjct: 158 VASGEPFGKAGAYAIQGRAAEFVERID 184
>gnl|CDD|166873 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 27.5 bits (61), Expect = 9.3
Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 415 EYLEGIDITLQKKIRELGVSEELCSIPGIDSKIKVALGENGIKTMEDLAGCSVDDLLGWS 474
+YLE + + ++ +RE + EL +P I K AL G +++ED+ +LL
Sbjct: 627 DYLETLHLRVKHGVREELL--ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELL--- 681
Query: 475 ENKGGNIEKFDGFLSSLGTPKDQVES 500
+ +G + +G LG K+
Sbjct: 682 KVEGIGAKIVEGIFKHLGVEKEVKIK 707
>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
Length = 486
Score = 27.3 bits (61), Expect = 9.8
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 134 FKDKVGEIISGTVKRVEYGNVIVDLG-NSDGVIRRDETISRENLRPGDRVK 183
F D G+I+ GTV +V+ V++D+G ++GVI E + ++ P + V+
Sbjct: 33 FND--GDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIKHDVDPNEVVE 81
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
0.317 0.136 0.375
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 8,708,441
Number of extensions: 596644
Number of successful extensions: 1347
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1325
Number of HSP's successfully gapped: 87
Length of query: 526
Length of database: 5,994,473
Length adjustment: 98
Effective length of query: 428
Effective length of database: 3,876,889
Effective search space: 1659308492
Effective search space used: 1659308492
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: 59 (26.5 bits)