Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012408921.1 NPUN_RS11850 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= SwissProt::Q9FV81 (550 letters) >NCBI__GCF_000020025.1:WP_012408921.1 Length = 491 Score = 542 bits (1397), Expect = e-158 Identities = 278/487 (57%), Positives = 358/487 (73%), Gaps = 12/487 (2%) Query: 69 DYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVR 128 +YEA+IG+ETH QLST TK F + S +G+ PNT+I PVCMGLPG LPVLN KV+E+ V+ Sbjct: 10 EYEAIIGLETHCQLSTKTKIFSNSSTAFGADPNTNIDPVCMGLPGVLPVLNEKVLEYAVK 69 Query: 129 LGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVD-IPLEFGGGHRRF 187 GLALNC ++ SKFDRKQYFYPDLPK YQISQ+D+PIA G+++++ + E +R Sbjct: 70 TGLALNCQIARYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWLEIELVDAEGNPSRKRI 129 Query: 188 GITRVHMEEDAGKLLHSDT-----GDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACE 242 GITR+HMEEDAGKL+H+ + YS VD NRAG+PL+EIVSEPD+RSG+EAAEYA E Sbjct: 130 GITRLHMEEDAGKLVHAGSDRLSGSSYSLVDYNRAGIPLVEIVSEPDLRSGLEAAEYAEE 189 Query: 243 MQRIARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEIS 302 ++RI RYLGVS+GNMQEGSLRCDVNIS+RP+G+ EFGTKVEIKN+N+FSAI RAID+EI Sbjct: 190 LRRIVRYLGVSDGNMQEGSLRCDVNISVRPVGRKEFGTKVEIKNMNSFSAIQRAIDYEIE 249 Query: 303 RQALLYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDS 362 RQ G D+I+ ETRLWEEGAQ+T +MR KEG +DYRYFPEPDL + ++ E +++ Sbjct: 250 RQIAAIEAG--DRIIQETRLWEEGAQRTSSMRVKEGSSDYRYFPEPDLAPIEVSNEQLEN 307 Query: 363 IRASLPELPEAKRRRYEA-MGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSD 421 R+ LPELP KR YE+ +GL D L D S+AEYF+ I GA K AANWI D Sbjct: 308 WRSELPELPAQKRHHYESELGLSAYDARVLTEDRSIAEYFETAIASGANPKAAANWITQD 367 Query: 422 IAAYLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAK 481 IAA+L +KL+I I+LTP LAE+I I+ G IS KE L +LL+ K Sbjct: 368 IAAHLNKQKLTITQIELTPTNLAEIITRIETGKISNAQAKEKLPDLLSGISPEKAF---A 424 Query: 482 DLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKI 541 L ITDP +E +V +V++ NPK+LE+YR+G T L+G+F GQV+K + +A+P L N++ Sbjct: 425 GLELITDPTVLEPIVDEVIAANPKELEKYRNGNTNLKGFFVGQVLKKTAKRADPKLTNEL 484 Query: 542 LLEKLNA 548 + +KLNA Sbjct: 485 VEKKLNA 491 Lambda K H 0.317 0.134 0.379 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 742 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 550 Length of database: 491 Length adjustment: 35 Effective length of query: 515 Effective length of database: 456 Effective search space: 234840 Effective search space used: 234840 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: 52 (24.6 bits)
Align candidate WP_012408921.1 NPUN_RS11850 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00133.hmm # target sequence database: /tmp/gapView.11600.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-186 605.4 0.0 3.6e-186 605.3 0.0 1.0 1 lcl|NCBI__GCF_000020025.1:WP_012408921.1 NPUN_RS11850 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_012408921.1 NPUN_RS11850 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 605.3 0.0 3.6e-186 3.6e-186 2 481 .] 9 490 .. 8 490 .. 0.98 Alignments for each domain: == domain 1 score: 605.3 bits; conditional E-value: 3.6e-186 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +eye++iGlE+H+ql tk+K+F+++s+ + pNtn++pvc+glPG+lPvlN+++++ A+k +laln+ lcl|NCBI__GCF_000020025.1:WP_012408921.1 9 TEYEAIIGLETHCQLSTKTKIFSNSSTAFGA-DPNTNIDPVCMGLPGVLPVLNEKVLEYAVKTGLALNC 76 79***************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgksq 134 +i +s+FdRK+YfYpDlPk+yqi+q+dlPiae+G leiel + e k+igi+rlh+EeD+gk++ lcl|NCBI__GCF_000020025.1:WP_012408921.1 77 QIA-RYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWLEIELVDAEgnpsrKRIGITRLHMEEDAGKLV 144 *65.6*************************************999899999****************** PP TIGR00133 135 ykesdk...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDv 200 +++sd+ +++slvD+NR+g+PL+EiV++Pdl+s+ ea+++ ++lr+i+ryl++sdg+++eGs+R+Dv lcl|NCBI__GCF_000020025.1:WP_012408921.1 145 HAGSDRlsgSSYSLVDYNRAGIPLVEIVSEPDLRSGLEAAEYAEELRRIVRYLGVSDGNMQEGSLRCDV 213 *****99999*********************************************************** PP TIGR00133 201 NvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKe 269 N+s+r++G++++gt+vEiKN+ns+++i++ai+yEieRq+++++ g+ + qetr ++e ++t s+R Ke lcl|NCBI__GCF_000020025.1:WP_012408921.1 214 NISVRPVGRKEFGTKVEIKNMNSFSAIQRAIDYEIERQIAAIEAGDRIIQETRLWEEGAQRTSSMRVKE 282 ********************************************************************* PP TIGR00133 270 eseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeev 338 s+DYRYfpePdl pie+++e++++ ++ +lpelP +kr+++++e+gls++da+vl++d++++++fe++ lcl|NCBI__GCF_000020025.1:WP_012408921.1 283 GSSDYRYFPEPDLAPIEVSNEQLEN-WRSELPELPAQKRHHYESELGLSAYDARVLTEDRSIAEYFETA 350 *********************9999.******************************************* PP TIGR00133 339 vklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkd 407 + ++pk+a+nWi+++++++Lnk+k+++++ l+p++lae+i i+ gkis+ +ake l ll+ ++ lcl|NCBI__GCF_000020025.1:WP_012408921.1 351 IASGANPKAAANWITQDIAAHLNKQKLTITQIELTPTNLAEIITRIETGKISNAQAKEKLPDLLSGISP 419 ***************************************************************998776 PP TIGR00133 408 pkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekll 476 k+ gl+ i+d++ l iv+evi+ npke+eky++g ++ +f+vGqv+kkt radpk +++l+ lcl|NCBI__GCF_000020025.1:WP_012408921.1 420 EKAF---AGLELITDPTVLEPIVDEVIAANPKELEKYRNGNTNLKGFFVGQVLKKTAKRADPKLTNELV 485 6665...58999********************************************************* PP TIGR00133 477 kells 481 +++l+ lcl|NCBI__GCF_000020025.1:WP_012408921.1 486 EKKLN 490 **996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (491 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 7.66 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory