Alignments for a candidate for gatA in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Allochromatium vinosum DSM 180

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_012972027.1 ALVIN_RS14240 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000025485.1:WP_012972027.1
          Length = 484

 Score =  489 bits (1260), Expect = e-143
 Identities = 245/460 (53%), Positives = 329/460 (71%), Gaps = 1/460 (0%)

Query: 24  DLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIV 83
           +L     +RI  +D  + +F+ +  E A A A+  D+ +    E G L G+PI  KD   
Sbjct: 22  ELTRHYLERIARLDPALNSFITVAAESALATAERADQTLRS-GEAGPLTGIPIAHKDIFC 80

Query: 84  TKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKN 143
           T+GL+T+C S++L+ F   YDAT+V+RL  A AV +GK NMDEFAMGSS E S Y   +N
Sbjct: 81  TQGLKTSCGSRMLDGFVAPYDATIVERLAAAGAVVLGKTNMDEFAMGSSNETSWYGPVRN 140

Query: 144 PWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVSRYGL 203
           PW+   VPGGSSGGSAAAVAA     +  SDTGGSIRQPA+ CGV G+KPTYGR SR+G+
Sbjct: 141 PWDAARVPGGSSGGSAAAVAARLCAAATASDTGGSIRQPAALCGVTGIKPTYGRCSRWGM 200

Query: 204 VAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGLKIAV 263
           +AFASSLDQ G + R+  D AF+L  ++G D+ DSTSA+V VPD++ +L  D+ GL+I +
Sbjct: 201 IAFASSLDQAGVMARSAADAAFILDEMAGFDERDSTSADVPVPDYVDALDDDLHGLRIGL 260

Query: 264 PKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASANLAR 323
           PKEY G G+     ++V+AA+K  E LGA   E+SLP+S  ++  YY+++ +E S+NLAR
Sbjct: 261 PKEYFGAGLDARIGDAVMAAIKEYEALGAEIVEISLPNSPLSVPVYYVVAPAECSSNLAR 320

Query: 324 FDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAYYKKAQKVRT 383
           FDG+RYG+R DN  +L DLY+++RAEGFG EV+RRIM+GT+ LS+GYYDAYY KAQK+R 
Sbjct: 321 FDGVRYGHRCDNPKDLQDLYERSRAEGFGPEVQRRIMIGTYVLSAGYYDAYYLKAQKIRQ 380

Query: 384 LIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLAGVPGISVPC 443
           LI  DF+  FE+ DVI+GPT+PT AF++G    DP++MY NDI TI  NLAG+PG+S+P 
Sbjct: 381 LIADDFKRAFEQVDVIMGPTSPTTAFQLGSKMDDPVSMYLNDIYTIATNLAGLPGMSIPV 440

Query: 444 GLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
              DGLP+GLQIIG +F E+ +  VAH ++ AT  H+A P
Sbjct: 441 EPVDGLPVGLQIIGNYFQEARLLNVAHRYQHATHWHQAAP 480


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: 581
Number of extensions: 20
Number of successful extensions: 1
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: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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_012972027.1 ALVIN_RS14240 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.32357.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     7e-188  611.0   0.0   8.1e-188  610.8   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012972027.1  ALVIN_RS14240 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012972027.1  ALVIN_RS14240 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.8   0.0  8.1e-188  8.1e-188       8     464 ..      16     473 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 610.8 bits;  conditional E-value: 8.1e-188
                                 TIGR00132   8 kevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdi 74 
                                               ++ s++e+++++leri + +  +n+f++v++e+al++a++ d++++  e  +l+gipia Kd ++++++
  lcl|NCBI__GCF_000025485.1:WP_012972027.1  16 RTYSSVELTRHYLERIARLDPALNSFITVAAESALATAERADQTLRsGEaGPLTGIPIAHKDIFCTQGL 84 
                                               67789999***********************************99975646****************** PP

                                 TIGR00132  75 ettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsg 143
                                               +t+c+S++L+++v+pydat+verl +aga+++GktN+DEFamGss etS +g+++nP++ +rvpGGSsg
  lcl|NCBI__GCF_000025485.1:WP_012972027.1  85 KTSCGSRMLDGFVAPYDATIVERLAAAGAVVLGKTNMDEFAMGSSNETSWYGPVRNPWDAARVPGGSSG 153
                                               ********************************************************************* PP

                                 TIGR00132 144 GsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedial 212
                                               Gsaaavaa l+  a +sDTGgSiRqPA++cgv G+KPtYG+ SR+G++a+asSldq G++a++  d+a+
  lcl|NCBI__GCF_000025485.1:WP_012972027.1 154 GSAAAVAARLCAAATASDTGGSIRQPAALCGVTGIKPTYGRCSRWGMIAFASSLDQAGVMARSAADAAF 222
                                               ********************************************************************* PP

                                 TIGR00132 213 vldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaei 281
                                               +ld+++g D++Dsts++v+v++++ +l +dl+gl++g+ ke+++ +ld ++ +++ +++++ e+lgaei
  lcl|NCBI__GCF_000025485.1:WP_012972027.1 223 ILDEMAGFDERDSTSADVPVPDYVDALDDDLHGLRIGLPKEYFGAGLDARIGDAVMAAIKEYEALGAEI 291
                                               ********************************************************************* PP

                                 TIGR00132 282 vevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGa 350
                                               ve+slp++ l++++Yy+++p+E ssnlar+dg+ryG+r +++k+l++ly ++R+egfg ev+rRim+G+
  lcl|NCBI__GCF_000025485.1:WP_012972027.1 292 VEISLPNSPLSVPVYYVVAPAECSSNLARFDGVRYGHRCDNPKDLQDLYERSRAEGFGPEVQRRIMIGT 360
                                               ********************************************************************* PP

                                 TIGR00132 351 yalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpan 419
                                               y+ls++yyd+yy+kAqk+r+li+d+f+ +fe+vDvi++pt+pt+af+lg+k++dp++myl+D++t+  n
  lcl|NCBI__GCF_000025485.1:WP_012972027.1 361 YVLSAGYYDAYYLKAQKIRQLIADDFKRAFEQVDVIMGPTSPTTAFQLGSKMDDPVSMYLNDIYTIATN 429
                                               ********************************************************************* PP

                                 TIGR00132 420 laGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                               laGlp++s+P++   +glp+Glqiig++f++ +ll+va+ +++a+
  lcl|NCBI__GCF_000025485.1:WP_012972027.1 430 LAGLPGMSIPVEPV-DGLPVGLQIIGNYFQEARLLNVAHRYQHAT 473
                                               *************9.7***********************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (484 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: 10.74
//
[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