Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate HSERO_RS23305 HSERO_RS23305 glutamyl-tRNA amidotransferase subunit A
Query= SwissProt::O06491 (485 letters) >FitnessBrowser__HerbieS:HSERO_RS23305 Length = 488 Score = 467 bits (1202), Expect = e-136 Identities = 246/489 (50%), Positives = 329/489 (67%), Gaps = 14/489 (2%) Query: 6 HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63 HK+T EL + ++I ++L RI A D + AFL +D E A AK D + Sbjct: 2 HKLTLKELSAQLQARKISATELATLFLDRIDASD--LNAFLHVDRELTLAQAKVADSRLS 59 Query: 64 GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123 + G L G+PI KD VT+G RTT S++L+N+ +DATVV++ A VT+GKLN Sbjct: 60 DNNA-GQLTGVPIAHKDIFVTRGWRTTAGSRMLDNYVSPFDATVVEQFNAAGMVTLGKLN 118 Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183 DEFAMGS ENS + T NPW+ VPGGSSGGSAAAVAA P + +DTGGSIRQPA Sbjct: 119 CDEFAMGSGNENSYFGPTLNPWDKRAVPGGSSGGSAAAVAARLAPAATATDTGGSIRQPA 178 Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243 S CGV G+KPTYG VSRYG++AFASSLDQ GPI +T ED LL A++G D+ DSTS Sbjct: 179 SLCGVTGIKPTYGSVSRYGMIAFASSLDQGGPIAKTAEDCGLLLNAMTGFDERDSTSLQR 238 Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303 DF SL ++GL+I VPKE+ G G+ + +V AAL E LGA E+SLP ++ Sbjct: 239 PKEDFTRSLNDSLQGLRIGVPKEFFGAGLAADVEAAVRAALSEFEKLGAQLVEISLPKTE 298 Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363 ++ YY+++ +EAS+NL+RFDG+RYG+R + NL D+Y+++RAEGFG EVKRRI++G+ Sbjct: 299 LSIPVYYVIAPAEASSNLSRFDGVRYGHRAADYGNLDDMYRKSRAEGFGEEVKRRILVGS 358 Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVF----EKYDVIVGPTTPTPAFKIGENTKDPL 419 + LS GYYDAYY +AQK+R LI +DF++ + DVI+GP +PT A+ +G+ T DP+ Sbjct: 359 YVLSHGYYDAYYLQAQKIRRLIAQDFQNALAGANRQCDVIMGPVSPTVAWDLGDKTNDPV 418 Query: 420 TMYANDILTIPVNLAGVPGISVPCGLADG-----LPLGLQIIGKHFDESTVYRVAHAFEQ 474 Y DI T+ +LAG+PG+S+PCG G P+GLQIIG +FDE+ + VAH F+Q Sbjct: 419 ANYLADIFTLSTSLAGLPGMSIPCGFGQGEKNGKRPVGLQIIGNYFDEARLLNVAHQFQQ 478 Query: 475 ATDHHKAKP 483 ATD H +P Sbjct: 479 ATDWHLREP 487 Lambda K H 0.315 0.134 0.381 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: 583 Number of extensions: 31 Number of successful extensions: 4 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: 485 Length of database: 488 Length adjustment: 34 Effective length of query: 451 Effective length of database: 454 Effective search space: 204754 Effective search space used: 204754 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 HSERO_RS23305 HSERO_RS23305 (glutamyl-tRNA amidotransferase subunit A)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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/TIGR00132.hmm # target sequence database: /tmp/gapView.11478.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-180 584.4 0.0 9.7e-180 584.2 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS23305 HSERO_RS23305 glutamyl-tRNA amid Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS23305 HSERO_RS23305 glutamyl-tRNA amidotransferase subunit A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 584.2 0.0 9.7e-180 9.7e-180 3 465 .. 11 481 .. 9 482 .. 0.97 Alignments for each domain: == domain 1 score: 584.2 bits; conditional E-value: 9.7e-180 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 ++l+++++s++e+++ +l+ri+a + +nafl+v++e +l++ak d++++ ++ +l+g+pia Kd lcl|FitnessBrowser__HerbieS:HSERO_RS23305 11 AQLQARKISATELATLFLDRIDASD--LNAFLHVDRELTLAQAKVADSRLSdNNaGQLTGVPIAHKDI 76 678999***************9865..6*********************9954435************ PP TIGR00132 69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136 +++++++tt++S++L+nyvsp+datVve+ ++ag++++Gk N DEFamGs+ e+S+fg+t nP++++ lcl|FitnessBrowser__HerbieS:HSERO_RS23305 77 FVTRGWRTTAGSRMLDNYVSPFDATVVEQFNAAGMVTLGKLNCDEFAMGSGNENSYFGPTLNPWDKRA 144 ******************************************************************** PP TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204 vpGGSsgGsaaavaa l+p a ++DTGgSiRqPAs+cgv G+KPtYG vSRyG++a+asSldq G++a lcl|FitnessBrowser__HerbieS:HSERO_RS23305 145 VPGGSSGGSAAAVAARLAPAATATDTGGSIRQPASLCGVTGIKPTYGSVSRYGMIAFASSLDQGGPIA 212 ******************************************************************** PP TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklle 272 k+ ed l+l++++g D++Dstsl+ ++e+++++l++ l+gl++gv ke+++ +l +v+++++++l lcl|FitnessBrowser__HerbieS:HSERO_RS23305 213 KTAEDCGLLLNAMTGFDERDSTSLQRPKEDFTRSLNDSLQGLRIGVPKEFFGAGLAADVEAAVRAALS 280 ******************************************************************** PP TIGR00132 273 kleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340 ++e+lga++ve+slp+ +l++++Yy+i+p+Eassnl+r+dg+ryG+r+ ++ +l+++y k+R+egfge lcl|FitnessBrowser__HerbieS:HSERO_RS23305 281 EFEKLGAQLVEISLPKTELSIPVYYVIAPAEASSNLSRFDGVRYGHRAADYGNLDDMYRKSRAEGFGE 348 ******************************************************************** PP TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklf....eevDvivsptaptlafklgekaed 404 evkrRi++G+y+ls++yyd+yy++Aqk+r+li+++f++++ +++Dvi++p++pt+a lg+k++d lcl|FitnessBrowser__HerbieS:HSERO_RS23305 349 EVKRRILVGSYVLSHGYYDAYYLQAQKIRRLIAQDFQNALaganRQCDVIMGPVSPTVAWDLGDKTND 416 ***************************************9999899********************** PP TIGR00132 405 plemylsDvltvpanlaGlpaisvPlgkke....kglpiGlqiigkafddkkllsvakaleqald 465 p+++yl+D++t+ +laGlp++s+P+g + p+Glqiig++fd+ +ll+va++++qa+d lcl|FitnessBrowser__HerbieS:HSERO_RS23305 417 PVANYLADIFTLSTSLAGLPGMSIPCGFGQgeknGKRPVGLQIIGNYFDEARLLNVAHQFQQATD 481 **************************86432221568************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (488 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: 10.27 // [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