Alignments for a candidate for gatA in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Desulfuromonas acetexigens

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_092055670.1 BQ4888_RS07090 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900111775.1:WP_092055670.1
          Length = 489

 Score =  548 bits (1413), Expect = e-160
 Identities = 278/489 (56%), Positives = 363/489 (74%), Gaps = 4/489 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M L D  I  L Q + ++EI   +L +    RI+A + ++ AF+ +  + AR  A   D+
Sbjct: 1   MELTDLTIHGLHQRLLRREITSLELTEAFLARIEASNPQLNAFITVTGDSARQAAAAADK 60

Query: 61  AVD---GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAV 117
            +    G  + G L G+P+ +KD  VT+G+RTTC+SKIL+NF P YD T V++L++  AV
Sbjct: 61  LLSSECGERKFGPLNGIPLALKDIFVTEGVRTTCASKILDNFIPPYDGTAVRKLKEQGAV 120

Query: 118 TIGKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGG 177
            +GKLNMDEFAMGSS E SA+   +NPWNLD V GGSSGGSAA+VAA +   +LG+DTGG
Sbjct: 121 ILGKLNMDEFAMGSSNETSAFGPVRNPWNLDCVAGGSSGGSAASVAALQTVAALGTDTGG 180

Query: 178 SIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMD 237
           SIRQPAS CGVVGLKPTYGRVSRYG++A+ASSLDQ+GP+TR VED A LL A++G D+ D
Sbjct: 181 SIRQPASHCGVVGLKPTYGRVSRYGVIAYASSLDQVGPVTRDVEDCAILLGAVAGHDRAD 240

Query: 238 STSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
           STS N  VPD+  +L   IKG+KI +PKEY  +G+  E R++   A++V   +GA + EV
Sbjct: 241 STSVNRAVPDYRKNLRQGIKGMKIGLPKEYFIDGLDPEVRQATDEAIRVCREMGAEFVEV 300

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLPH+ YA+A YYL++++EAS+NL+R+DG+R+G R D    LID+Y ++RA GFG+EVKR
Sbjct: 301 SLPHTAYAVACYYLVATAEASSNLSRYDGVRFGLRVDEGQGLIDMYMKSRAAGFGDEVKR 360

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
           RIMLGT+ALSSGYYDAYY KAQKVRTLI++DF D F + DV++ P  PTPAFKIGE T D
Sbjct: 361 RIMLGTYALSSGYYDAYYLKAQKVRTLIRQDFLDAFNQVDVLLTPVAPTPAFKIGEKTAD 420

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQAT 476
           PL MY +DI TIPVNLAG   +S+PCGL+  GLP+GLQ+IG+ F E T+ + A+AFEQAT
Sbjct: 421 PLQMYLSDIFTIPVNLAGTCALSLPCGLSSAGLPIGLQLIGRPFGEETILQAAYAFEQAT 480

Query: 477 DHHKAKPEL 485
           D HK  P +
Sbjct: 481 DWHKQAPNI 489


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: 633
Number of extensions: 28
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: 489
Length adjustment: 34
Effective length of query: 451
Effective length of database: 455
Effective search space:   205205
Effective search space used:   205205
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_092055670.1 BQ4888_RS07090 (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.10114.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-197  641.0   0.0   6.3e-197  640.8   0.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092055670.1  BQ4888_RS07090 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092055670.1  BQ4888_RS07090 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 !  640.8   0.0  6.3e-197  6.3e-197       2     465 ..      12     481 ..      11     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 640.8 bits;  conditional E-value: 6.3e-197
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.....ke.kklagipia 64 
                                               ++ l ++e+++ e++e++l+riea + ++naf++vt ++a ++a++ dk ++     ++  +l+gip+a
  lcl|NCBI__GCF_900111775.1:WP_092055670.1  12 HQRLLRREITSLELTEAFLARIEASNPQLNAFITVTGDSARQAAAAADKLLSsecgeRKfGPLNGIPLA 80 
                                               678999***********************************999999998777776433459******* PP

                                 TIGR00132  65 vKdniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPen 133
                                               +Kd +++++++ttcaSkiL+n+++pyd t v++lke+ga+i+Gk N+DEFamGss etSafg+++nP+n
  lcl|NCBI__GCF_900111775.1:WP_092055670.1  81 LKDIFVTEGVRTTCASKILDNFIPPYDGTAVRKLKEQGAVILGKLNMDEFAMGSSNETSAFGPVRNPWN 149
                                               ********************************************************************* PP

                                 TIGR00132 134 eervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGi 202
                                                + v+GGSsgGsaa+vaa + + alg+DTGgSiRqPAs+cgvvGlKPtYG+vSRyG++ayasSldq+G+
  lcl|NCBI__GCF_900111775.1:WP_092055670.1 150 LDCVAGGSSGGSAASVAALQTVAALGTDTGGSIRQPASHCGVVGLKPTYGRVSRYGVIAYASSLDQVGP 218
                                               ********************************************************************* PP

                                 TIGR00132 203 lakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekll 271
                                               ++++ved a++l +++g+D +Dsts++ +v+++ ++l++ +kg+k+g+ ke++ ++ld ev+++ ++++
  lcl|NCBI__GCF_900111775.1:WP_092055670.1 219 VTRDVEDCAILLGAVAGHDRADSTSVNRAVPDYRKNLRQGIKGMKIGLPKEYFIDGLDPEVRQATDEAI 287
                                               ********************************************************************* PP

                                 TIGR00132 272 ekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                               ++ +e+gae+vevslp+  +a+a Yy+++++Eassnl+rydg+r+G rv+e + l ++y+k+R++gfg+
  lcl|NCBI__GCF_900111775.1:WP_092055670.1 288 RVCREMGAEFVEVSLPHTAYAVACYYLVATAEASSNLSRYDGVRFGLRVDEGQGLIDMYMKSRAAGFGD 356
                                               ********************************************************************* PP

                                 TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemy 409
                                               evkrRimlG+yals++yyd+yy+kAqkvrtli+++f ++f++vDv+++p+apt afk+gek++dpl+my
  lcl|NCBI__GCF_900111775.1:WP_092055670.1 357 EVKRRIMLGTYALSSGYYDAYYLKAQKVRTLIRQDFLDAFNQVDVLLTPVAPTPAFKIGEKTADPLQMY 425
                                               ********************************************************************* PP

                                 TIGR00132 410 lsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               lsD++t+p+nlaG++a+s+P+g ++ glpiGlq+ig+ f ++++l++a+a+eqa+d
  lcl|NCBI__GCF_900111775.1:WP_092055670.1 426 LSDIFTIPVNLAGTCALSLPCGLSSAGLPIGLQLIGRPFGEETILQAAYAFEQATD 481
                                               *****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (489 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: 00:00:00.02
# Mc/sec: 10.20
//
[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