Alignments for a candidate for gatB in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfovibrio gracilis DSM 16080

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_078717533.1 B5D49_RS09865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_900167125.1:WP_078717533.1
          Length = 477

 Score =  447 bits (1150), Expect = e-130
 Identities = 224/483 (46%), Positives = 321/483 (66%), Gaps = 8/483 (1%)

Query: 67  LRDYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFG 126
           +  YE VIG+E H QL T +K FC+CS  +G+ PN ++CPVC G+PG LPV+N KV+E+ 
Sbjct: 1   MAQYEVVIGLEVHAQLKTESKLFCACSTRFGNDPNENVCPVCSGMPGVLPVMNEKVLEYA 60

Query: 127 VRLGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRR 186
            +LGLA++C+++ KS F RK YFYPDLPKGYQ SQFD+PI   G     I +E   G + 
Sbjct: 61  AKLGLAVDCEINRKSVFARKNYFYPDLPKGYQTSQFDLPICEHGR----IVIETSKGRKT 116

Query: 187 FGITRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRI 246
            G+TR+HMEEDAGK +HS + + S VDLNRA VPL+EIVSEPDMRS  EA  Y   +  I
Sbjct: 117 IGVTRIHMEEDAGKSIHSASENVSFVDLNRACVPLVEIVSEPDMRSAEEAVAYLKSLHSI 176

Query: 247 ARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQAL 306
            RYL + +GNM++GS RCD N+SIRP GQ EFGT+ E+KN+N+F  + +AID+EI RQ  
Sbjct: 177 LRYLDICDGNMEQGSFRCDANVSIRPRGQKEFGTRTELKNMNSFRHVQKAIDYEIERQID 236

Query: 307 LYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRAS 366
           L   G+A  ++ ETRL+      T +MR KE   DYRYFP PDL  ++L + ++   R  
Sbjct: 237 LVEDGEA--VIQETRLYNADKGTTHSMRGKEEAHDYRYFPCPDLVPMVLDEAWIAQWRDE 294

Query: 367 LPELPEAKRRRY-EAMGLGMQDVLFLANDVSVAEYFD-AVIGKGAEVKLAANWIMSDIAA 424
           LPELP  +R R+    GL  +  + L ++   A++F+ A     ++ K  ANW+M D+A 
Sbjct: 295 LPELPTVRRERFLLEYGLAEETAVQLTSERETADFFEVAARAATSKPKKIANWVMVDVAH 354

Query: 425 YLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAKDLV 484
            L    LS+ + K +P+ LA L+  ++ GT+S K  K+IL E+L  G   K ++K K L 
Sbjct: 355 LLNESGLSLAECKGSPEYLAALVDLVEGGTVSAKSAKDILSEVLRDGADPKALVKEKGLA 414

Query: 485 QITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKILLE 544
           Q +D   +E ++ +V++ENP + E+ R+G  K+ G+  GQ+M+ ++GKANPG+++K+L +
Sbjct: 415 QESDTGALEAVIEEVITENPDEAERVRAGDKKVIGFLMGQIMRKTQGKANPGVVSKMLAQ 474

Query: 545 KLN 547
           KL+
Sbjct: 475 KLS 477


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: 674
Number of extensions: 34
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: 550
Length of database: 477
Length adjustment: 35
Effective length of query: 515
Effective length of database: 442
Effective search space:   227630
Effective search space used:   227630
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_078717533.1 B5D49_RS09865 (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.1190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-187  608.4   0.0   4.4e-187  608.3   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078717533.1  B5D49_RS09865 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078717533.1  B5D49_RS09865 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 !  608.3   0.0  4.4e-187  4.4e-187       1     480 [.       1     476 [.       1     477 [] 0.98

  Alignments for each domain:
  == domain 1  score: 608.3 bits;  conditional E-value: 4.4e-187
                                 TIGR00133   1 kieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                               + +ye+viGlEvH ql t+sKlFc cs+++ +  pN+nvcpvc g+PG+lPv+N+++++ A kl+la++
  lcl|NCBI__GCF_900167125.1:WP_078717533.1   1 MAQYEVVIGLEVHAQLKTESKLFCACSTRFGN-DPNENVCPVCSGMPGVLPVMNEKVLEYAAKLGLAVD 68 
                                               679*****************************.9*********************************** PP

                                 TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykes 138
                                               ++i+  +svF+RK+YfYpDlPkgyq +q+dlPi+e+G++ ie++++ k+ig++r+h+EeD+gks +  s
  lcl|NCBI__GCF_900167125.1:WP_078717533.1  69 CEIN-RKSVFARKNYFYPDLPKGYQTSQFDLPICEHGRIVIETSKGRKTIGVTRIHMEEDAGKSIHSAS 136
                                               **77.59************************************************************88 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                               +  + s+vD+NR++vPL+EiV++Pd++sa+ea+a+lk+l++ilryl+i dg++e+Gs+R+D+Nvsir++
  lcl|NCBI__GCF_900167125.1:WP_078717533.1 137 E--NVSFVDLNRACVPLVEIVSEPDMRSAEEAVAYLKSLHSILRYLDICDGNMEQGSFRCDANVSIRPR 203
                                               5..8***************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                               Gq+++gtr E+KN+ns++ ++kai+yEieRq++l+++ge v qetr ++  k +t s+R Kee++DYRY
  lcl|NCBI__GCF_900167125.1:WP_078717533.1 204 GQKEFGTRTELKNMNSFRHVQKAIDYEIERQIDLVEDGEAVIQETRLYNADKGTTHSMRGKEEAHDYRY 272
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fp Pdl+p+++de ++ + ++ +lpelP+ +r+r+  eygl ee a  l+s++e +d fe ++++++++
  lcl|NCBI__GCF_900167125.1:WP_078717533.1 273 FPCPDLVPMVLDEAWIAQ-WRDELPELPTVRRERFLLEYGLAEETAVQLTSERETADFFEVAARAATSK 340
                                               ******************.*****************************************998876544 PP

                                 TIGR00133 346 .klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklie 413
                                                k+ +nW++ +++  Ln++ +slae+  +pe+la+l++l++ g++s+ksak++l+e+l ++ dpk+l++
  lcl|NCBI__GCF_900167125.1:WP_078717533.1 341 pKKIANWVMVDVAHLLNESGLSLAECKGSPEYLAALVDLVEGGTVSAKSAKDILSEVLRDGADPKALVK 409
                                               4******************************************************************** PP

                                 TIGR00133 414 klgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ++gl q sd+ +l +++eevi+enp+e e+ ++g +k+++fl+Gq+m+kt+g+a+p  v k+l ++l
  lcl|NCBI__GCF_900167125.1:WP_078717533.1 410 EKGLAQESDTGALEAVIEEVITENPDEAERVRAGDKKVIGFLMGQIMRKTQGKANPGVVSKMLAQKL 476
                                               **************************************************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (477 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: 00:00:00.03
# Mc/sec: 7.56
//
[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