Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate Synpcc7942_0118 Synpcc7942_0118 aspartyl/glutamyl-tRNA amidotransferase subunit B
Query= SwissProt::Q9FV81 (550 letters) >FitnessBrowser__SynE:Synpcc7942_0118 Length = 494 Score = 544 bits (1402), Expect = e-159 Identities = 277/485 (57%), Positives = 364/485 (75%), Gaps = 9/485 (1%) Query: 69 DYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVR 128 +YEAVIG+ETHVQL T TK F + S +G+ PNT I PV +GLPG LPVLN KV+E+ V+ Sbjct: 10 EYEAVIGLETHVQLGTATKIFSNASTEFGADPNTHIDPVVLGLPGTLPVLNQKVLEYAVK 69 Query: 129 LGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGH-RRF 187 GLALNC ++ SKFDRKQYFYPDLPK YQISQ+D+PIA G++++++ + + ++ Sbjct: 70 AGLALNCQIAPYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWIEIEVAEKGKEPYTKKI 129 Query: 188 GITRVHMEEDAGKLLHSDT-----GDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACE 242 G+TR+HMEEDAGKL+H+ + +S VD NRAGV L EIVSEPD+R+G EAAEYA E Sbjct: 130 GVTRLHMEEDAGKLVHAGSDRLAGSTHSLVDYNRAGVALAEIVSEPDLRTGKEAAEYAQE 189 Query: 243 MQRIARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEIS 302 ++RI RYLGVS+GNM EGSLRCDVNISIRP G +FGTKVEIKN+N+F+AI RAI+FEI Sbjct: 190 LRRIMRYLGVSDGNMAEGSLRCDVNISIRPKGTEKFGTKVEIKNMNSFNAIQRAIEFEIE 249 Query: 303 RQALLYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDS 362 RQ G + IV ETRLW+EG Q T +MR KEG +DYRYFPEPDL + +++ ++ Sbjct: 250 RQIRCLETG--EPIVQETRLWDEGKQVTKSMRSKEGSSDYRYFPEPDLGPIEVSETQRET 307 Query: 363 IRASLPELPEAKRRRY-EAMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSD 421 R+ LPELP KR RY E GL D L ++ S A+Y++A + GA+ K AANW+M D Sbjct: 308 WRSELPELPAQKRHRYAEQYGLSAYDARVLTDEKSTADYYEATVAAGADAKQAANWLMGD 367 Query: 422 IAAYLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAK 481 IAAY+ KL ++D+ L PQ+LAEL+ I+ GTISGKI KEIL ELL KGG+ K +++AK Sbjct: 368 IAAYVNANKLLVSDLPLQPQDLAELVNLIEAGTISGKIAKEILPELLEKGGSPKAIVEAK 427 Query: 482 DLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKI 541 L QI+DPA+IE +V ++++ +P +LEQ+R+GKTKLQG+F GQ+MK + G+ +P L N+I Sbjct: 428 GLTQISDPAQIEALVDELLAAHPTELEQFRAGKTKLQGFFVGQLMKKTGGRVDPKLSNQI 487 Query: 542 LLEKL 546 L +KL Sbjct: 488 LNQKL 492 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: 800 Number of extensions: 33 Number of successful extensions: 5 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: 494 Length adjustment: 35 Effective length of query: 515 Effective length of database: 459 Effective search space: 236385 Effective search space used: 236385 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 Synpcc7942_0118 Synpcc7942_0118 (aspartyl/glutamyl-tRNA amidotransferase 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.10270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-193 628.2 0.0 4.7e-193 628.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0118 Synpcc7942_0118 aspartyl/glutamy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0118 Synpcc7942_0118 aspartyl/glutamyl-tRNA amidotransferase subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 628.0 0.0 4.7e-193 4.7e-193 2 480 .. 9 492 .. 8 493 .. 0.98 Alignments for each domain: == domain 1 score: 628.0 bits; conditional E-value: 4.7e-193 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 +eye+viGlE+Hvql+t++K+F+++s+e+ pNt+++pv lglPG+lPvlN+++++ A+k +laln+ lcl|FitnessBrowser__SynE:Synpcc7942_0118 9 TEYEAVIGLETHVQLGTATKIFSNASTEFGA-DPNTHIDPVVLGLPGTLPVLNQKVLEYAVKAGLALNC 76 79***************************99.9************************************ PP TIGR00133 71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.....keigierlhlEeDtgksq 134 + ++++s+FdRK+YfYpDlPk+yqi+q+dlPiae+G +eie+ ek k+ig++rlh+EeD+gk++ lcl|FitnessBrowser__SynE:Synpcc7942_0118 77 Q-IAPYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWIEIEVAEKGkepytKKIGVTRLHMEEDAGKLV 144 *.668************************************9987678999****************** PP TIGR00133 135 ykesdk...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDv 200 +++sd+ +++slvD+NR+gv L EiV++Pdl+++kea+++ ++lr+i+ryl++sdg++ eGs+R+Dv lcl|FitnessBrowser__SynE:Synpcc7942_0118 145 HAGSDRlagSTHSLVDYNRAGVALAEIVSEPDLRTGKEAAEYAQELRRIMRYLGVSDGNMAEGSLRCDV 213 *****99999*********************************************************** PP TIGR00133 201 NvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKe 269 N+sir+kG+ek+gt+vEiKN+ns+++i++aie+EieRq++ l++ge ++qetr +de k++t s+R+Ke lcl|FitnessBrowser__SynE:Synpcc7942_0118 214 NISIRPKGTEKFGTKVEIKNMNSFNAIQRAIEFEIERQIRCLETGEPIVQETRLWDEGKQVTKSMRSKE 282 ********************************************************************* PP TIGR00133 270 eseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeev 338 s+DYRYfpePdl pie++e++ +e+++ +lpelP +kr+r+ ++ygls++da+vl+++++ +d++e lcl|FitnessBrowser__SynE:Synpcc7942_0118 283 GSSDYRYFPEPDLGPIEVSETQ-RETWRSELPELPAQKRHRYAEQYGLSAYDARVLTDEKSTADYYEAT 350 ********************97.666******************************************* PP TIGR00133 339 vklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkd 407 v + +++k+a+nW++ ++++++n++k+ +++ l+p++lael++li++g+is+k+ake+l elle++++ lcl|FitnessBrowser__SynE:Synpcc7942_0118 351 VAAGADAKQAANWLMGDIAAYVNANKLLVSDLPLQPQDLAELVNLIEAGTISGKIAKEILPELLEKGGS 419 ********************************************************************* PP TIGR00133 408 pkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekll 476 pk+++e++gl+qisd+ ++ ++v+e ++ +p e+e++++gk k+++f+vGq mkkt gr+dpk +++l lcl|FitnessBrowser__SynE:Synpcc7942_0118 420 PKAIVEAKGLTQISDPAQIEALVDELLAAHPTELEQFRAGKTKLQGFFVGQLMKKTGGRVDPKLSNQIL 488 ********************************************************************* PP TIGR00133 477 kell 480 +++l lcl|FitnessBrowser__SynE:Synpcc7942_0118 489 NQKL 492 9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (494 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: 00:00:00.02 # Mc/sec: 8.61 // [ok]
This GapMind analysis is from Apr 09 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