Alignments for a candidate for gatA in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Xenophilus azovorans DSM 13620

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_038210743.1 Q392_RS18225 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000745855.1:WP_038210743.1
          Length = 495

 Score =  463 bits (1192), Expect = e-135
 Identities = 240/486 (49%), Positives = 327/486 (67%), Gaps = 11/486 (2%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  L + +  +E+   +       R++A  D + AF+++DEE   A A+  D A+    +
Sbjct: 10  VAALARALAAREVSAEEAARHFLGRMKAHQD-LAAFVSVDEEATLAQARAADAAL-AAGK 67

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+PI  KD  VT G  +T  S++L ++   +DATVV++L  A  VT+GKL+ DEF
Sbjct: 68  AGPLAGVPIAHKDIFVTTGWPSTAGSRMLADYRSPFDATVVRKLAGAGMVTLGKLSCDEF 127

Query: 128 AMGSSTEN--------SAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSI 179
           AMGS+ EN         A    +NPW+ + VPGGSSGGSA AVAA   P + G+DTGGSI
Sbjct: 128 AMGSANENVAVPAAGLDAVSPVRNPWDRERVPGGSSGGSAVAVAAALAPAATGTDTGGSI 187

Query: 180 RQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDK-MDS 238
           RQPASFCG+ G+KPTYGR SRYG++AFASSLDQ GP+ R+ ED A LL A+ G D   DS
Sbjct: 188 RQPASFCGITGIKPTYGRASRYGMIAFASSLDQAGPMARSAEDCALLLSAMCGPDPDRDS 247

Query: 239 TSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVS 298
           TS +V   DF   L   ++GL+I VPKE++GEGV    R ++ AAL   E LGA   EVS
Sbjct: 248 TSLDVPAEDFSRQLHASLEGLRIGVPKEFVGEGVAPGVRAAIEAALAEYEKLGARRVEVS 307

Query: 299 LPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRR 358
           LP ++ ++  YY+L+++EAS+NL+RFDG+++G+R     +L ++Y +TRAEGFG+EVKRR
Sbjct: 308 LPRTELSIPVYYILAAAEASSNLSRFDGVKFGHRAAQYKDLAEMYAKTRAEGFGDEVKRR 367

Query: 359 IMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDP 418
           IM+GT+ LS GYYDAYY +AQKVR +I  DF+  F   DVI GP  PT A+KIGE+  DP
Sbjct: 368 IMIGTYVLSHGYYDAYYLQAQKVRRMIADDFQQAFRDCDVIAGPAAPTVAWKIGEHGGDP 427

Query: 419 LTMYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478
           +  Y  D+ T+P +LAG+PG+SVPCG    +P+GLQ+IG +F E+ +   AH F+QATD 
Sbjct: 428 VADYLADVFTLPASLAGLPGMSVPCGFDGSMPVGLQLIGNYFGEAKLLNAAHRFQQATDW 487

Query: 479 HKAKPE 484
           H+  PE
Sbjct: 488 HRKTPE 493


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: 602
Number of extensions: 23
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: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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_038210743.1 Q392_RS18225 (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.12300.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-171  556.0   0.0     4e-171  555.8   0.0    1.0  1  lcl|NCBI__GCF_000745855.1:WP_038210743.1  Q392_RS18225 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038210743.1  Q392_RS18225 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 !  555.8   0.0    4e-171    4e-171       3     465 ..      15     486 ..      13     487 .. 0.96

  Alignments for each domain:
  == domain 1  score: 555.8 bits;  conditional E-value: 4e-171
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                               ++l ++evs++e+++++l r++a++d + af++v++e +l++a++ d+++a  +  +lag+pia Kd +
  lcl|NCBI__GCF_000745855.1:WP_038210743.1  15 RALAAREVSAEEAARHFLGRMKAHQD-LAAFVSVDEEATLAQARAADAALAaGKaGPLAGVPIAHKDIF 82 
                                               568899********************.**********************9975537************* PP

                                 TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSa........fgvtkn 130
                                               ++ +++ t++S++L +y+sp+datVv++l  ag++++Gk   DEFamGs+ e+ a          +++n
  lcl|NCBI__GCF_000745855.1:WP_038210743.1  83 VTTGWPSTAGSRMLADYRSPFDATVVRKLAGAGMVTLGKLSCDEFAMGSANENVAvpaagldaVSPVRN 151
                                               **************************************************9986422222222689*** PP

                                 TIGR00132 131 PeneervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldq 199
                                               P+++ervpGGSsgGsa avaa l+p a g+DTGgSiRqPAsfcg+ G+KPtYG+ SRyG++a+asSldq
  lcl|NCBI__GCF_000745855.1:WP_038210743.1 152 PWDRERVPGGSSGGSAVAVAAALAPAATGTDTGGSIRQPASFCGITGIKPTYGRASRYGMIAFASSLDQ 220
                                               ********************************************************************* PP

                                 TIGR00132 200 iGilakkvedialvldvisgkD.kkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekf 267
                                                G++a++ ed al+l++++g D  +Dstsl+v+ e++ ++l++ l gl++gv ke+ +e++  +v++++
  lcl|NCBI__GCF_000745855.1:WP_038210743.1 221 AGPMARSAEDCALLLSAMCGPDpDRDSTSLDVPAEDFSRQLHASLEGLRIGVPKEFVGEGVAPGVRAAI 289
                                               **********************559******************************************** PP

                                 TIGR00132 268 ekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRse 336
                                               e++l + e+lga  vevslp+ +l++++Yyi++ +Eassnl+r+dg+++G+r+ ++k+l e+yaktR+e
  lcl|NCBI__GCF_000745855.1:WP_038210743.1 290 EAALAEYEKLGARRVEVSLPRTELSIPVYYILAAAEASSNLSRFDGVKFGHRAAQYKDLAEMYAKTRAE 358
                                               ********************************************************************* PP

                                 TIGR00132 337 gfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedp 405
                                               gfg+evkrRim+G+y+ls++yyd+yy++Aqkvr++i+d+f+++f+++Dvi++p+apt+a k+ge+  dp
  lcl|NCBI__GCF_000745855.1:WP_038210743.1 359 GFGDEVKRRIMIGTYVLSHGYYDAYYLQAQKVRRMIADDFQQAFRDCDVIAGPAAPTVAWKIGEHGGDP 427
                                               ********************************************************************* PP

                                 TIGR00132 406 lemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               ++ yl+Dv+t+pa+laGlp++svP+g +   +p+Glq+ig++f + kll++a+ ++qa+d
  lcl|NCBI__GCF_000745855.1:WP_038210743.1 428 VADYLADVFTLPASLAGLPGMSVPCGFD-GSMPVGLQLIGNYFGEAKLLNAAHRFQQATD 486
                                               ****************************.69*************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (495 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: 7.98
//
[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