Alignments for a candidate for gatA in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Saccharomonospora cyanea NA-134

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_005454204.1 SACCYDRAFT_RS05035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000244975.1:WP_005454204.1
          Length = 502

 Score =  453 bits (1166), Expect = e-132
 Identities = 247/475 (52%), Positives = 319/475 (67%), Gaps = 9/475 (1%)

Query: 10  ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEH- 68
           EL + IH +E+   ++      RI  VD  V AFL +D + A A A+ +DE++ G  E  
Sbjct: 11  ELAEKIHSREVSSEEVTQAHLDRIAEVDSDVHAFLHVDADGALAAARTVDESLAGGGEPT 70

Query: 69  GLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFA 128
             L G+P+ +KD   T  + TTC S+ LEN+ P YDATV ++L++A    +GK NMDEFA
Sbjct: 71  SALAGVPLALKDVFTTSDMPTTCGSRTLENWVPPYDATVTRKLREAGVPILGKTNMDEFA 130

Query: 129 MGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGV 188
           MGSSTENSA+  T+NPW+ + VPGGS GGS+A++AA E P ++G+DTGGSIRQPA+  G 
Sbjct: 131 MGSSTENSAFGPTRNPWDRERVPGGSGGGSSASLAAFEAPLAIGTDTGGSIRQPAAVTGT 190

Query: 189 VGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDF 248
           VG+KPTYG VSRYGLVAF+SSLDQ GP  RTV D A L + I+G D +DSTS ++ VP  
Sbjct: 191 VGVKPTYGGVSRYGLVAFSSSLDQGGPCARTVLDAALLHEVIAGHDPLDSTSIDMPVPPV 250

Query: 249 L----SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           +        GD+ G+K+ V +E  GEG       S  AA+  L  LGA   EVS P+  Y
Sbjct: 251 VRAAREGARGDLTGVKVGVVRELSGEGYQAGVLASFDAAVARLRELGAEIVEVSCPNFSY 310

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYR-TDNADNLI-DLYKQTRAEGFGNEVKRRIMLG 362
            L+ YYL++ SE S+NLARFD +RYG R +D+ D+   ++   +R  GFG EVKRRIMLG
Sbjct: 311 GLSAYYLIAPSECSSNLARFDAMRYGLRVSDDGDHSAEEVMSASREAGFGPEVKRRIMLG 370

Query: 363 TFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMY 422
           T+ALSSGYYDAYY  AQKVRTLI +DF   FE+ DV+V PTTPT AF++GE   DPL MY
Sbjct: 371 TYALSSGYYDAYYGSAQKVRTLIARDFTAAFEQVDVLVSPTTPTTAFRLGERVDDPLAMY 430

Query: 423 ANDILTIPVNLAGVPGISVPCGLA--DGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
             D+ TIP NLAG   +SVP GL+  DGLP+GLQI+     +  +YRV  A+E A
Sbjct: 431 LADLATIPANLAGNAAMSVPSGLSDDDGLPVGLQIMAPALADERLYRVGAAYEAA 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: 636
Number of extensions: 29
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: 502
Length adjustment: 34
Effective length of query: 451
Effective length of database: 468
Effective search space:   211068
Effective search space used:   211068
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_005454204.1 SACCYDRAFT_RS05035 (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.7760.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-191  623.6   0.0   1.2e-191  623.4   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454204.1  SACCYDRAFT_RS05035 Asp-tRNA(Asn)


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454204.1  SACCYDRAFT_RS05035 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit Gat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.4   0.0  1.2e-191  1.2e-191       2     463 ..      13     485 ..      12     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 623.4 bits;  conditional E-value: 1.2e-191
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.k.klagipiavK 66 
                                               +e+++++evs++ev+++ l+ri +v+++++afl+v+++ al++a+ +d+++a   e +  lag+p+a+K
  lcl|NCBI__GCF_000244975.1:WP_005454204.1  13 AEKIHSREVSSEEVTQAHLDRIAEVDSDVHAFLHVDADGALAAARTVDESLAggGEpTsALAGVPLALK 81 
                                               67899**********************************************999444459********* PP

                                 TIGR00132  67 dniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPenee 135
                                               d++++ d++ttc+S++Len+v+pydatV+++l+eag+ i+GktN+DEFamGsste+Safg+t+nP+++e
  lcl|NCBI__GCF_000244975.1:WP_005454204.1  82 DVFTTSDMPTTCGSRTLENWVPPYDATVTRKLREAGVPILGKTNMDEFAMGSSTENSAFGPTRNPWDRE 150
                                               ********************************************************************* PP

                                 TIGR00132 136 rvpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGila 204
                                               rvpGGS+gGs+a++aa+++pla+g+DTGgSiRqPA+++g+vG+KPtYG vSRyGlva++sSldq G++a
  lcl|NCBI__GCF_000244975.1:WP_005454204.1 151 RVPGGSGGGSSASLAAFEAPLAIGTDTGGSIRQPAAVTGTVGVKPTYGGVSRYGLVAFSSSLDQGGPCA 219
                                               ********************************************************************* PP

                                 TIGR00132 205 kkvedialvldvisgkDkkDstslevkveelleelkk....dlkglkvgvvkelseesldkevkekfek 269
                                               ++v d+al+++vi+g+D  Dsts++++v+ +++++++    dl g+kvgvv+els+e+++ +v ++f++
  lcl|NCBI__GCF_000244975.1:WP_005454204.1 220 RTVLDAALLHEVIAGHDPLDSTSIDMPVPPVVRAAREgargDLTGVKVGVVRELSGEGYQAGVLASFDA 288
                                               *****************************999888887778999************************* PP

                                 TIGR00132 270 llekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelks..lkelyaktRse 336
                                               ++ +l+elgaeivevs+p++++ l++Yy+i+psE ssnlar+d++ryG rv+++ +  ++e+++++R++
  lcl|NCBI__GCF_000244975.1:WP_005454204.1 289 AVARLRELGAEIVEVSCPNFSYGLSAYYLIAPSECSSNLARFDAMRYGLRVSDDGDhsAEEVMSASREA 357
                                               ****************************************************998777999******** PP

                                 TIGR00132 337 gfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedp 405
                                               gfg evkrRimlG+yals++yyd+yy  Aqkvrtli+++f+ +fe+vDv+vspt+pt+af+lge+ +dp
  lcl|NCBI__GCF_000244975.1:WP_005454204.1 358 GFGPEVKRRIMLGTYALSSGYYDAYYGSAQKVRTLIARDFTAAFEQVDVLVSPTTPTTAFRLGERVDDP 426
                                               ********************************************************************* PP

                                 TIGR00132 406 lemylsDvltvpanlaGlpaisvPlgkke.kglpiGlqiigkafddkkllsvakaleqa 463
                                               l+myl+D+ t+panlaG+ a+svP g ++ +glp+Glqi++ a++d++l++v++a+e+a
  lcl|NCBI__GCF_000244975.1:WP_005454204.1 427 LAMYLADLATIPANLAGNAAMSVPSGLSDdDGLPVGLQIMAPALADERLYRVGAAYEAA 485
                                               *************************9877589***********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (502 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: 8.11
//
[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