Alignments for a candidate for gatA in Trichodesmium erythraeum IMS101

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Trichodesmium erythraeum IMS101

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011611677.1 TERY_RS09795 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000014265.1:WP_011611677.1
          Length = 485

 Score =  530 bits (1365), Expect = e-155
 Identities = 255/482 (52%), Positives = 364/482 (75%), Gaps = 4/482 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I+++ Q +  K+    ++  E+ + I  ++ K+++F+ +  E+A A A+++D  +    +
Sbjct: 4   ISDIHQQLISKQRSAVEITQEALENINQLEPKLKSFICVTAEKAIAQARQVDAKIAAGEK 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            GLL G+PI VKDNI T+G+ TTC SKIL+NF P Y++TV Q+L DA A+ +GK N+DEF
Sbjct: 64  IGLLTGIPIAVKDNICTRGIPTTCGSKILQNFIPPYESTVTQKLVDAGAIILGKTNLDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
            MGSSTENSAY++T NPW+   VPGGSSGGSAAAVA+ E   +LGSDTGGSIRQPASFCG
Sbjct: 124 GMGSSTENSAYQVTTNPWDNTRVPGGSSGGSAAAVASAESVVALGSDTGGSIRQPASFCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVG+KPTYG VSRYGLVA+ASS+DQIGP++RTV+D+A LLQAI+G D  DSTS NV VPD
Sbjct: 184 VVGIKPTYGLVSRYGLVAYASSMDQIGPLSRTVKDSAILLQAIAGYDPKDSTSLNVPVPD 243

Query: 248 FLSSLTGDIK---GLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKY 304
           +  +LT +++    ++I + +E  G+G+     ++   A+++++ LGA  + +S P   Y
Sbjct: 244 YTKNLTPNLRPKGQIRIGLIQETFGDGLDSSVLQAFTKAVELMQELGAEIQVISCPRFSY 303

Query: 305 ALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTF 364
            L TYY+++ SEASANLAR+DG++YG+R   ++NL+++Y +TR+EGFG+EVKRRIM+GT+
Sbjct: 304 GLPTYYVIAPSEASANLARYDGVKYGFRASESENLLNMYAKTRSEGFGSEVKRRIMIGTY 363

Query: 365 ALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAN 424
           ALS+GYYDAYY KAQKVRTLIK+DF+  F K D++  PT+PT AFK+GE + +PL+MY +
Sbjct: 364 ALSAGYYDAYYLKAQKVRTLIKEDFDKAFAKVDILACPTSPTTAFKLGEKSDNPLSMYLS 423

Query: 425 DILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483
           D++TIPVNLAG+P +S+PCG    GLP+G+Q+I     E  ++  A+ +EQA + +K +P
Sbjct: 424 DLMTIPVNLAGLPALSLPCGFDQQGLPIGMQLISNVLKEDLLFEAAYVYEQANNWYKFQP 483

Query: 484 EL 485
           +L
Sbjct: 484 QL 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: 617
Number of extensions: 23
Number of successful extensions: 3
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_011611677.1 TERY_RS09795 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.28048.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-205  668.8   0.0   2.4e-205  668.6   0.0    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011611677.1  TERY_RS09795 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011611677.1  TERY_RS09795 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.6   0.0  2.4e-205  2.4e-205       2     463 ..       8     475 ..       7     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 668.6 bits;  conditional E-value: 2.4e-205
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..ke.kklagipiavKd 67 
                                               +++l +k+ s++e+++e le+i++ + k+++f+ vt+eka+++a+++d+k+a  ++  +l+gipiavKd
  lcl|NCBI__GCF_000014265.1:WP_011611677.1   8 HQQLISKQRSAVEITQEALENINQLEPKLKSFICVTAEKAIAQARQVDAKIAagEKiGLLTGIPIAVKD 76 
                                               688999999******************************************9964556*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                               ni++++i+ttc+SkiL+n+++py++tV+++l +aga+i+GktNlDEF+mGsste+Sa++vt+nP++++r
  lcl|NCBI__GCF_000014265.1:WP_011611677.1  77 NICTRGIPTTCGSKILQNFIPPYESTVTQKLVDAGAIILGKTNLDEFGMGSSTENSAYQVTTNPWDNTR 145
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaava  + ++algsDTGgSiRqPAsfcgvvG+KPtYGlvSRyGlvayasS+dqiG+l++
  lcl|NCBI__GCF_000014265.1:WP_011611677.1 146 VPGGSSGGSAAAVASAESVVALGSDTGGSIRQPASFCGVVGIKPTYGLVSRYGLVAYASSMDQIGPLSR 214
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlk...glkvgvvkelseesldkevkekfekll 271
                                               +v+d a++l++i+g+D kDstsl+v+v++++++l+ +l+   ++++g+++e ++++ld++v ++f k++
  lcl|NCBI__GCF_000014265.1:WP_011611677.1 215 TVKDSAILLQAIAGYDPKDSTSLNVPVPDYTKNLTPNLRpkgQIRIGLIQETFGDGLDSSVLQAFTKAV 283
                                               **********************************9965533379************************* PP

                                 TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                               e ++elgaei+ +s+p++++ l++Yy+i+psEas+nlarydg++yG r++e ++l ++yaktRsegfg+
  lcl|NCBI__GCF_000014265.1:WP_011611677.1 284 ELMQELGAEIQVISCPRFSYGLPTYYVIAPSEASANLARYDGVKYGFRASESENLLNMYAKTRSEGFGS 352
                                               ********************************************************************* PP

                                 TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemy 409
                                               evkrRim+G+yals++yyd+yy+kAqkvrtli+++f+k+f +vD++++pt+pt+afklgek ++pl+my
  lcl|NCBI__GCF_000014265.1:WP_011611677.1 353 EVKRRIMIGTYALSAGYYDAYYLKAQKVRTLIKEDFDKAFAKVDILACPTSPTTAFKLGEKSDNPLSMY 421
                                               ********************************************************************* PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               lsD++t+p+nlaGlpa+s+P+g +++glpiG+q+i+++++++ l+++a+ +eqa
  lcl|NCBI__GCF_000014265.1:WP_011611677.1 422 LSDLMTIPVNLAGLPALSLPCGFDQQGLPIGMQLISNVLKEDLLFEAAYVYEQA 475
                                               ****************************************************97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.86
//
[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