Alignments for a candidate for gatA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Marinobacter adhaerens HP15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate GFF2513 HP15_2457 glutamyl-tRNA (Gln) amidotransferase A subunit

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__Marino:GFF2513
          Length = 485

 Score =  512 bits (1319), Expect = e-150
 Identities = 259/486 (53%), Positives = 342/486 (70%), Gaps = 5/486 (1%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  + EL + +   +I   +L  E   RI+  D K  +F+ + EE+A A A+  DE  
Sbjct: 1   MHNKSVAELSRELESGKISSVELTQEFLDRIKREDSKYNSFITVTEEQALADARVADEQR 60

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
              +      G+P   KD   T G+RTTC SK+LENF P YDATV    ++A AV +GK 
Sbjct: 61  AAGNATPWT-GVPFAHKDIFCTNGVRTTCGSKMLENFVPPYDATVTANFREAGAVCLGKT 119

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDT----VPGGSSGGSAAAVAAGEVPFSLGSDTGGS 178
           NMDEFAMGSS ENS +    NPW L      VPGGSSGGSAAAVAA  +P +  +DTGGS
Sbjct: 120 NMDEFAMGSSNENSYFGAVTNPWGLSEGNKRVPGGSSGGSAAAVAARLIPAATATDTGGS 179

Query: 179 IRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDS 238
           IRQPA+ CGV GLKPTYGRVSRYG++AFASSLDQ G + RT EDNA +L  ++G D  DS
Sbjct: 180 IRQPAALCGVTGLKPTYGRVSRYGMIAFASSLDQGGTMARTAEDNALMLNVMAGFDPKDS 239

Query: 239 TSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVS 298
           TS + +VPD+ ++L   +KGL+I +P+EY  + +     + V  A+K  E LGAT +EVS
Sbjct: 240 TSIDREVPDYTATLNEPLKGLRIGLPREYFSDQLSPAMEQQVRNAVKEYEKLGATVKEVS 299

Query: 299 LPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRR 358
           LP++K A+A YY+++ +EASANL+RFDG+RYGYR +N  +L+DLY ++RAEGFG EVKRR
Sbjct: 300 LPNAKLAIAAYYVIAPAEASANLSRFDGVRYGYRCENPKDLMDLYTRSRAEGFGEEVKRR 359

Query: 359 IMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDP 418
           I++GT+ALS+GY+DAYY KAQKVR LI++DF + F++ DV++ PTTP+PAF  GE T DP
Sbjct: 360 ILVGTYALSAGYFDAYYLKAQKVRRLIQQDFINAFKEVDVLMSPTTPSPAFIQGEKTSDP 419

Query: 419 LTMYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDH 478
           +TMY  D+ TI +NLAGVP +SVP G  DGLP+GLQIIG +F E+ +   AH F+Q TD 
Sbjct: 420 VTMYLEDVFTIAINLAGVPAMSVPAGFVDGLPVGLQIIGDYFSEARLLNAAHQFQQVTDW 479

Query: 479 HKAKPE 484
           H+ KP+
Sbjct: 480 HQRKPQ 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: 574
Number of extensions: 19
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 GFF2513 HP15_2457 (glutamyl-tRNA (Gln) amidotransferase A subunit)
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.3605661.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.9e-188  611.8   0.0   4.5e-188  611.7   0.0    1.0  1  FitnessBrowser__Marino:GFF2513  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF2513  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.7   0.0  4.5e-188  4.5e-188       4     465 ..      12     478 ..       9     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 611.7 bits;  conditional E-value: 4.5e-188
                       TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiettcaS 80 
                                      l++ ++s++e+++e+l+ri++ ++k+n+f++vt+e+al+ a+  d++ a  + ++ +g+p+a Kd +++++++ttc+S
  FitnessBrowser__Marino:GFF2513  12 ELESGKISSVELTQEFLDRIKREDSKYNSFITVTEEQALADARVADEQRAaGNaTPWTGVPFAHKDIFCTNGVRTTCGS 90 
                                     5677899***************************************999875547************************ PP

                       TIGR00132  81 kiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknP....eneervpGGSsgGsaaavaadlvp 155
                                     k+Len+v+pydatV+ + +eaga+ +GktN+DEFamGss e+S+fg+++nP    e ++rvpGGSsgGsaaavaa l+p
  FitnessBrowser__Marino:GFF2513  91 KMLENFVPPYDATVTANFREAGAVCLGKTNMDEFAMGSSNENSYFGAVTNPwglsEGNKRVPGGSSGGSAAAVAARLIP 169
                                     ***************************************************44444689******************** PP

                       TIGR00132 156 lalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslevkvee 234
                                      a ++DTGgSiRqPA++cgv GlKPtYG+vSRyG++a+asSldq G +a++ ed al+l+v++g D kDsts++ +v++
  FitnessBrowser__Marino:GFF2513 170 AATATDTGGSIRQPAALCGVTGLKPTYGRVSRYGMIAFASSLDQGGTMARTAEDNALMLNVMAGFDPKDSTSIDREVPD 248
                                     ******************************************************************************* PP

                       TIGR00132 235 lleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydg 313
                                     ++ +l++ lkgl++g+ +e++ ++l+ ++++++++++++ e+lga+++evslp+ kla+a+Yy+i+p+Eas+nl+r+dg
  FitnessBrowser__Marino:GFF2513 249 YTATLNEPLKGLRIGLPREYFSDQLSPAMEQQVRNAVKEYEKLGATVKEVSLPNAKLAIAAYYVIAPAEASANLSRFDG 327
                                     ******************************************************************************* PP

                       TIGR00132 314 iryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptap 392
                                     +ryG+r e++k+l++ly+++R+egfgeevkrRi++G+yals++y+d+yy+kAqkvr+li+++f ++f+evDv++spt+p
  FitnessBrowser__Marino:GFF2513 328 VRYGYRCENPKDLMDLYTRSRAEGFGEEVKRRILVGTYALSAGYFDAYYLKAQKVRRLIQQDFINAFKEVDVLMSPTTP 406
                                     ******************************************************************************* PP

                       TIGR00132 393 tlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                       af  gek++dp++myl+Dv+t+ +nlaG+pa+svP+g   +glp+Glqiig +f++ +ll++a++++q +d
  FitnessBrowser__Marino:GFF2513 407 SPAFIQGEKTSDPVTMYLEDVFTIAINLAGVPAMSVPAGFV-DGLPVGLQIIGDYFSEARLLNAAHQFQQVTD 478
                                     *****************************************.7*************************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: 15.89
//
[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