Alignments for a candidate for gatA in Hyphomicrobium sulfonivorans WDL6

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Hyphomicrobium sulfonivorans WDL6

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_068460249.1 APY04_RS04815 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_001541235.1:WP_068460249.1
          Length = 500

 Score =  476 bits (1224), Expect = e-138
 Identities = 247/484 (51%), Positives = 328/484 (67%), Gaps = 13/484 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I E +  + KKE+  ++L       I+  + ++ A++    E A   A+E D  +     
Sbjct: 9   IAEARDKLRKKEVSATELTQAFIDAIEVANPQLNAYVRTTPELALKQAEESDRRLKSGDA 68

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             L  G+P+G KD   TK + TT  SKILE F P Y++TV   L +A AV +GKLN DEF
Sbjct: 69  RPLE-GLPLGNKDLFCTKDVETTACSKILEGFTPTYESTVGSNLWNAGAVMLGKLNCDEF 127

Query: 128 AMGSSTENSAYKLTKNPWNL----------DTVPGGSSGGSAAAVAAGEVPFSLGSDTGG 177
           AMGSS E SAY    +PW            + VPGGSSGGS+AAVAA     +  +DTGG
Sbjct: 128 AMGSSNETSAYGPVVSPWRRAGADGQLTSENLVPGGSSGGSSAAVAADLCLGATATDTGG 187

Query: 178 SIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMD 237
           SIRQPA+  G VG+KPTYGR SR+G+VAFASSLDQ GP+ +TV D A +L++++  D  D
Sbjct: 188 SIRQPAALTGTVGIKPTYGRCSRWGIVAFASSLDQAGPLAKTVRDAAIMLRSMASHDPKD 247

Query: 238 STSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
           STS    VPD+  +L   +KGL++ VPKEY  EG+  +        ++ L+  GAT  EV
Sbjct: 248 STSVETPVPDYELALAQGVKGLRVGVPKEYRVEGMSPDIERLWQEGIEWLKAAGATIHEV 307

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLPH+K+AL TYY+++ +EAS+NLAR+DG+RYG R +  D LID+Y+ +RA GFG EV+R
Sbjct: 308 SLPHTKFALPTYYVVAPAEASSNLARYDGVRYGLRVEGKD-LIDMYENSRAAGFGKEVQR 366

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
           R+++GT+ LS+GYYDAYY KAQKVRTLIK+DF+D ++  DV++ PTTPTPAFKIGE   D
Sbjct: 367 RVLIGTYVLSAGYYDAYYLKAQKVRTLIKRDFDDAWQSVDVLLTPTTPTPAFKIGEKLDD 426

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLA-DGLPLGLQIIGKHFDESTVYRVAHAFEQAT 476
           P+ MYA DI T+ VN+AG+PGISVP G++ DGLPLGLQ+IGK FDE+T++R A   E A 
Sbjct: 427 PMAMYAQDIFTVTVNMAGLPGISVPAGISVDGLPLGLQLIGKPFDEATLFRAAQVIEDAA 486

Query: 477 DHHK 480
            H K
Sbjct: 487 GHFK 490


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: 656
Number of extensions: 24
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: 500
Length adjustment: 34
Effective length of query: 451
Effective length of database: 466
Effective search space:   210166
Effective search space used:   210166
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_068460249.1 APY04_RS04815 (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.2330518.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-176  571.7   0.0   6.9e-176  571.5   0.0    1.0  1  NCBI__GCF_001541235.1:WP_068460249.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001541235.1:WP_068460249.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  571.5   0.0  6.9e-176  6.9e-176       2     463 ..      13     485 ..      12     488 .. 0.98

  Alignments for each domain:
  == domain 1  score: 571.5 bits;  conditional E-value: 6.9e-176
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 
                                           +++l kkevs++e++++++++ie  + ++na++++t+e alk+a+++d++++  + ++l g+p++ Kd +++k
  NCBI__GCF_001541235.1:WP_068460249.1  13 RDKLRKKEVSATELTQAFIDAIEVANPQLNAYVRTTPELALKQAEESDRRLKsGDaRPLEGLPLGNKDLFCTK 85 
                                           57899**********************************************964436**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP..........enee 135
                                           d+ett+ SkiLe+++++y++tV  +l +aga+++Gk N DEFamGss etSa+g++  P          + e+
  NCBI__GCF_001541235.1:WP_068460249.1  86 DVETTACSKILEGFTPTYESTVGSNLWNAGAVMLGKLNCDEFAMGSSNETSAYGPVVSPwrragadgqlTSEN 158
                                           ***********************************************************77777776666789 PP

                             TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                            vpGGSsgGs+aavaadl+  a ++DTGgSiRqPA+++g+vG+KPtYG+ SR+G+va+asSldq G+lak+v 
  NCBI__GCF_001541235.1:WP_068460249.1 159 LVPGGSSGGSSAAVAADLCLGATATDTGGSIRQPAALTGTVGIKPTYGRCSRWGIVAFASSLDQAGPLAKTVR 231
                                           9************************************************************************ PP

                             TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaei 281
                                           d+a++l  ++ +D kDsts+e++v+++  +l++ +kgl+vgv ke++ e+++ ++++ +++ +e l++ ga+i
  NCBI__GCF_001541235.1:WP_068460249.1 232 DAAIMLRSMASHDPKDSTSVETPVPDYELALAQGVKGLRVGVPKEYRVEGMSPDIERLWQEGIEWLKAAGATI 304
                                           ************************************************************************* PP

                             TIGR00132 282 vevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayals 354
                                            evslp+ k+al++Yy+++p+Eassnlarydg+ryG rve ++ l ++y ++R++gfg+ev+rR+++G+y+ls
  NCBI__GCF_001541235.1:WP_068460249.1 305 HEVSLPHTKFALPTYYVVAPAEASSNLARYDGVRYGLRVEGKD-LIDMYENSRAAGFGKEVQRRVLIGTYVLS 376
                                           ***************************************9988.***************************** PP

                             TIGR00132 355 keyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpais 427
                                           ++yyd+yy+kAqkvrtli+++f++++++vDv+++pt+pt afk+gek +dp++my++D++tv++n+aGlp+is
  NCBI__GCF_001541235.1:WP_068460249.1 377 AGYYDAYYLKAQKVRTLIKRDFDDAWQSVDVLLTPTTPTPAFKIGEKLDDPMAMYAQDIFTVTVNMAGLPGIS 449
                                           ************************************************************************* PP

                             TIGR00132 428 vPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                           vP+g + +glp+Glq+igk fd+ +l+++a+ +e+a
  NCBI__GCF_001541235.1:WP_068460249.1 450 VPAGISVDGLPLGLQLIGKPFDEATLFRAAQVIEDA 485
                                           *******************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (500 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: 00:00:00.00
# Mc/sec: 25.08
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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