Alignments for a candidate for gatA in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfatibacillum aliphaticivorans DSM 15576

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_028316044.1 G491_RS0121615 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000429905.1:WP_028316044.1
          Length = 485

 Score =  546 bits (1406), Expect = e-160
 Identities = 275/487 (56%), Positives = 359/487 (73%), Gaps = 4/487 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M+L +  I + ++ +  KEI   DL      RI+AV+ +V A+L + +E A   A++ D+
Sbjct: 1   MALHELTIGQAREKLLSKEISSQDLTKAVLDRIEAVEPQVDAYLTVSKEEAMEAAQKADK 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
           A+  + E   L G+P+ +KD + TKG+ TTC+SKIL NF P YDAT + +L++A AV +G
Sbjct: 61  AL-AQGETAPLCGIPLAIKDVMCTKGVPTTCASKILGNFVPPYDATSITKLKEAGAVLVG 119

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           K NMDEFAMGSSTENSA+K TKNPW+L   PGGSSGGSAAAVAA     + GSDTGGSIR
Sbjct: 120 KTNMDEFAMGSSTENSAFKTTKNPWDLTRTPGGSSGGSAAAVAADMCLGAFGSDTGGSIR 179

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QP S C VVGLKPTYGRVSRYGLVAFASSLDQIGP  +TVED A LLQA++G D  DSTS
Sbjct: 180 QPGSHCSVVGLKPTYGRVSRYGLVAFASSLDQIGPFAKTVEDAAILLQAVAGYDPSDSTS 239

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLG-EGVGKEARESVLAALKVLEGLGATWEEVSL 299
            NV+VPD+ +++  D+KG+++ +PKEY    G+  + + SV  A+K LE  G    EVSL
Sbjct: 240 VNVEVPDYTTAIQEDVKGMRVGMPKEYFEMGGLTPDVKNSVDQAIKTLESQGVEVMEVSL 299

Query: 300 PHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRI 359
           PHSKY +A YY+++ +EAS+NLAR+DG++YG R +  D+LID+Y  TR+ GFG EV+RRI
Sbjct: 300 PHSKYCVAVYYVIAPAEASSNLARYDGVKYGMR-EERDSLIDMYHATRSSGFGPEVQRRI 358

Query: 360 MLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPL 419
           ++GT+ALS+GYYDAYY KA +VRTLI +D++  FEK D I+ P  PTPAFK+GENT DPL
Sbjct: 359 IIGTYALSAGYYDAYYGKASQVRTLIMEDYKKAFEKCDAIISPVAPTPAFKLGENTDDPL 418

Query: 420 TMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478
           TMY +DI T+  NLAGV G+SVPCG  ++GLP+GLQ+ G HF E  + R+ H F++ATD 
Sbjct: 419 TMYLSDIFTLSANLAGVCGVSVPCGFSSEGLPIGLQLQGSHFQEEKILRLGHHFQKATDF 478

Query: 479 HKAKPEL 485
           H  +P L
Sbjct: 479 HTKRPNL 485


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: 618
Number of extensions: 24
Number of successful extensions: 5
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: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
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_028316044.1 G491_RS0121615 (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.3430003.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-201  656.3   0.1   1.5e-201  656.1   0.1    1.0  1  NCBI__GCF_000429905.1:WP_028316044.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000429905.1:WP_028316044.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.1   0.1  1.5e-201  1.5e-201       2     465 ..      12     477 ..      11     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 656.1 bits;  conditional E-value: 1.5e-201
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 
                                           +e+l +ke+s++++++++l+rieav+ +++a+l+v+ke+a+++a+k dk++a  e  +l gip+a+Kd++++k
  NCBI__GCF_000429905.1:WP_028316044.1  12 REKLLSKEISSQDLTKAVLDRIEAVEPQVDAYLTVSKEEAMEAAQKADKALAqGEtAPLCGIPLAIKDVMCTK 84 
                                           578899********************************************9975535**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145
                                           +++ttcaSkiL n+v+pydat +++lkeaga+++GktN+DEFamGsste+Saf+ tknP++ +r pGGSsgGs
  NCBI__GCF_000429905.1:WP_028316044.1  85 GVPTTCASKILGNFVPPYDATSITKLKEAGAVLVGKTNMDEFAMGSSTENSAFKTTKNPWDLTRTPGGSSGGS 157
                                           ************************************************************************* PP

                             TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218
                                           aaavaad++  a gsDTGgSiRqP s+c+vvGlKPtYG+vSRyGlva+asSldqiG++ak+ved+a++l++++
  NCBI__GCF_000429905.1:WP_028316044.1 158 AAAVAADMCLGAFGSDTGGSIRQPGSHCSVVGLKPTYGRVSRYGLVAFASSLDQIGPFAKTVEDAAILLQAVA 230
                                           ************************************************************************* PP

                             TIGR00132 219 gkDkkDstslevkveelleelkkdlkglkvgvvkelsee.sldkevkekfekllekleelgaeivevslpsvk 290
                                           g+D  Dsts++v+v+++++++++d+kg++vg+ ke++e  +l  +vk+++++++++le++g+e++evslp++k
  NCBI__GCF_000429905.1:WP_028316044.1 231 GYDPSDSTSVNVEVPDYTTAIQEDVKGMRVGMPKEYFEMgGLTPDVKNSVDQAIKTLESQGVEVMEVSLPHSK 303
                                           ***********************************999735999***************************** PP

                             TIGR00132 291 lalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyyk 363
                                           +++a+Yy+i+p+Eassnlarydg++yG+r e ++ l ++y +tRs+gfg ev+rRi++G+yals++yyd+yy 
  NCBI__GCF_000429905.1:WP_028316044.1 304 YCVAVYYVIAPAEASSNLARYDGVKYGMREERDS-LIDMYHATRSSGFGPEVQRRIIIGTYALSAGYYDAYYG 375
                                           *****************************77666.************************************** PP

                             TIGR00132 364 kAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekg 436
                                           kA +vrtli+++++k+fe++D i+sp+apt afklge+++dpl+mylsD++t+ anlaG++++svP+g +++g
  NCBI__GCF_000429905.1:WP_028316044.1 376 KASQVRTLIMEDYKKAFEKCDAIISPVAPTPAFKLGENTDDPLTMYLSDIFTLSANLAGVCGVSVPCGFSSEG 448
                                           ************************************************************************* PP

                             TIGR00132 437 lpiGlqiigkafddkkllsvakaleqald 465
                                           lpiGlq++g +f+++k+l++++++++a+d
  NCBI__GCF_000429905.1:WP_028316044.1 449 LPIGLQLQGSHFQEEKILRLGHHFQKATD 477
                                           ************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (485 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: 00:00:00.01
# Mc/sec: 14.71
//
[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