Alignments for a candidate for gatB in Trichormus variabilis ATCC 29413

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Trichormus variabilis ATCC 29413

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011320645.1 AVA_RS20035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000204075.1:WP_011320645.1
          Length = 491

 Score =  525 bits (1351), Expect = e-153
 Identities = 271/486 (55%), Positives = 358/486 (73%), Gaps = 12/486 (2%)

Query: 69  DYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVR 128
           +YEA+IG+ETH QLST TK F S S  +G+ PNT+I PVCMGLPG LPVLN KV+E+ V+
Sbjct: 10  EYEAIIGLETHCQLSTNTKIFSSSSTAFGADPNTNIDPVCMGLPGVLPVLNEKVLEYAVK 69

Query: 129 LGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVD-IPLEFGGGHRRF 187
            GLALNC ++  SKFDRKQYFYPDLPK YQISQ+D+PIA  G+++++ +  E     +R 
Sbjct: 70  AGLALNCQIAKYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWLEIELLDAEGNPKRKRI 129

Query: 188 GITRVHMEEDAGKLLHSDT-----GDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACE 242
           GITR+HMEEDAGKL+H+ +       YS VD NRAGVPL+EIVSEPD+R+G EAAEYA E
Sbjct: 130 GITRLHMEEDAGKLVHAGSDRISGSTYSLVDYNRAGVPLVEIVSEPDIRTGQEAAEYAQE 189

Query: 243 MQRIARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEIS 302
           ++R+ RYLGVS+GNMQEGSLRCDVNIS+RP+GQ +FGTKVEIKN+N+FSAI +AI+ EI 
Sbjct: 190 LRRVMRYLGVSDGNMQEGSLRCDVNISVRPVGQEKFGTKVEIKNMNSFSAIQKAIEHEIE 249

Query: 303 RQALLYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDS 362
           RQ      G  ++I+ ETRLWEEG+Q+T++MR KEG +DYRYFPEPDL  + +++  +  
Sbjct: 250 RQIEAIESG--EKIIQETRLWEEGSQRTISMRTKEGSSDYRYFPEPDLAPIEVSEAQLSQ 307

Query: 363 IRASLPELPEAKRRRYEA-MGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSD 421
            R  LPELP  KR RYE+ +GL   D   L  DV+V++YF+A I  GA  K AANWI  D
Sbjct: 308 WRGELPELPAQKRHRYESELGLSAYDTRVLTEDVTVSQYFEAAIASGANPKAAANWITQD 367

Query: 422 IAAYLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAK 481
           IAAYL  +KLSI +I LTP  LA++I  I+ G IS    K+ L ELL  G + +     +
Sbjct: 368 IAAYLNKQKLSIAEIGLTPANLADVITRIETGKISNAQAKQKLPELLT-GLSPEKAFAGQ 426

Query: 482 DLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKI 541
           +L  I+D + +E +V +V++ NPK+LE+YR+G   L+G+F GQV+K +  +A+P L N++
Sbjct: 427 EL--ISDLSVLEPIVDEVIAANPKELEKYRNGNINLKGFFVGQVLKKTNKRADPKLTNEL 484

Query: 542 LLEKLN 547
           + +KLN
Sbjct: 485 VEKKLN 490


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: 760
Number of extensions: 36
Number of successful extensions: 6
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_011320645.1 AVA_RS20035 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
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.12045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-187  607.6   0.0   7.9e-187  607.4   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011320645.1  AVA_RS20035 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011320645.1  AVA_RS20035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.4   0.0  7.9e-187  7.9e-187       2     481 .]       9     490 ..       8     490 .. 0.97

  Alignments for each domain:
  == domain 1  score: 607.4 bits;  conditional E-value: 7.9e-187
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +eye++iGlE+H+ql t++K+F+++s+ +    pNtn++pvc+glPG+lPvlN+++++ A+k +laln+
  lcl|NCBI__GCF_000204075.1:WP_011320645.1   9 TEYEAIIGLETHCQLSTNTKIFSSSSTAFGA-DPNTNIDPVCMGLPGVLPVLNEKVLEYAVKAGLALNC 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_000204075.1:WP_011320645.1  77 QI-AKYSKFDRKQYFYPDLPKNYQISQYDLPIAEHGWLEIELLDAEgnpkrKRIGITRLHMEEDAGKLV 144
                                               *5.57************************************9988888999****************** PP

                                 TIGR00133 135 ykesdk...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDv 200
                                               +++sd+   +++slvD+NR+gvPL+EiV++Pd+++++ea+++ ++lr+++ryl++sdg+++eGs+R+Dv
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 145 HAGSDRisgSTYSLVDYNRAGVPLVEIVSEPDIRTGQEAAEYAQELRRVMRYLGVSDGNMQEGSLRCDV 213
                                               *****99999*********************************************************** PP

                                 TIGR00133 201 NvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKe 269
                                               N+s+r++Gqek+gt+vEiKN+ns+++i+kaie+EieRq++++++ge++ qetr ++e +++t+s+R Ke
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 214 NISVRPVGQEKFGTKVEIKNMNSFSAIQKAIEHEIERQIEAIESGEKIIQETRLWEEGSQRTISMRTKE 282
                                               ********************************************************************* PP

                                 TIGR00133 270 eseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeev 338
                                                s+DYRYfpePdl pie++e ++++ ++++lpelP +kr+r+++e+gls++d++vl++d+++ ++fe +
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 283 GSSDYRYFPEPDLAPIEVSEAQLSQ-WRGELPELPAQKRHRYESELGLSAYDTRVLTEDVTVSQYFEAA 350
                                               **********************999.******************************************* PP

                                 TIGR00133 339 vklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkd 407
                                                 + ++pk+a+nWi+++++++Lnk+k+s+ae  l+p +la +i  i+ gkis+ +ak+ l ell+  + 
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 351 IASGANPKAAANWITQDIAAYLNKQKLSIAEIGLTPANLADVITRIETGKISNAQAKQKLPELLTGLS- 418
                                               **************************************************************998655. PP

                                 TIGR00133 408 pkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekll 476
                                               p+k    +  + isd + l  iv+evi+ npke+eky++g  ++ +f+vGqv+kkt+ radpk +++l+
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 419 PEKAFAGQ--ELISDLSVLEPIVDEVIAANPKELEKYRNGNINLKGFFVGQVLKKTNKRADPKLTNELV 485
                                               55544444..5589******************************************************* PP

                                 TIGR00133 477 kells 481
                                               +++l+
  lcl|NCBI__GCF_000204075.1:WP_011320645.1 486 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.63
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis