Alignments for a candidate for gatA in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Geobacter metallireducens GS-15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_004514199.1 GMET_RS00375 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000012925.1:WP_004514199.1
          Length = 485

 Score =  563 bits (1451), Expect = e-165
 Identities = 279/483 (57%), Positives = 363/483 (75%), Gaps = 2/483 (0%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           M LFD  I EL   + +KE+   +       RI+AVD KV A++ +  E A A A+  D 
Sbjct: 1   MELFDLTIHELHDRLKRKELSSVEATRAMLARIEAVDPKVNAYITVTPEEALAAAEAADR 60

Query: 61  AVDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIG 120
            +    +   L G+P+ +KD  VTKG+RTTC+SKIL+NF P YD T V +L++A AV +G
Sbjct: 61  RI-AAGDMAPLTGIPVALKDIFVTKGIRTTCASKILDNFVPPYDGTAVAKLKEAGAVIVG 119

Query: 121 KLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIR 180
           KLN DEFAMGSS E+SA+  T+NPWNL+ +PGGSS GSAAA+AA     +LG+DTGGSIR
Sbjct: 120 KLNQDEFAMGSSGESSAFGPTRNPWNLECIPGGSSSGSAAAIAARTATATLGTDTGGSIR 179

Query: 181 QPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTS 240
           QPAS CG VGL+PTYGRVSRYG++A+ASSLDQ+GP+TR V D A +LQA++G D MDSTS
Sbjct: 180 QPASHCGCVGLRPTYGRVSRYGVIAYASSLDQVGPVTRDVTDCALMLQAVAGHDPMDSTS 239

Query: 241 ANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLP 300
             V VPD+   LTGD+KGLK+ +PKEY  EG+  + ++++  A++   GLGA + ++SLP
Sbjct: 240 VEVPVPDYAKGLTGDVKGLKLGLPKEYYIEGLDPDVKKALDEAIETYRGLGAEFVDISLP 299

Query: 301 HSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIM 360
           H+ YA+ATYYL++++EAS+NLAR++G+R+G+RT+ A NLID++++TR+EGFG+EVKRRIM
Sbjct: 300 HTDYAVATYYLIATAEASSNLARYEGVRFGHRTEGAANLIDMFRKTRSEGFGDEVKRRIM 359

Query: 361 LGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLT 420
           +GT+ALSSGYYDAYY KAQKVRTLI +DF   FE  D I+ P  PTPAFKIGE T DPL 
Sbjct: 360 IGTYALSSGYYDAYYLKAQKVRTLIMQDFLKAFEAVDAILTPVAPTPAFKIGEKTSDPLR 419

Query: 421 MYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           MY +DI TIPVNLAG   +SVP G++  GLP+GLQ+IG+ F E T+ R AHAFEQAT  H
Sbjct: 420 MYLSDIFTIPVNLAGTCAVSVPAGMSGAGLPIGLQLIGRPFGEETILRAAHAFEQATAWH 479

Query: 480 KAK 482
             K
Sbjct: 480 TQK 482


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: 620
Number of extensions: 35
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_004514199.1 GMET_RS00375 (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.8119.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-197  641.7   0.0     4e-197  641.5   0.0    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004514199.1  GMET_RS00375 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004514199.1  GMET_RS00375 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 !  641.5   0.0    4e-197    4e-197       2     464 ..      12     476 ..      11     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 641.5 bits;  conditional E-value: 4e-197
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                               ++ lk+ke+s++e+++++l+rieav+ k+na+++vt+e+al++a++ d+++a  +  +l+gip+a+Kd 
  lcl|NCBI__GCF_000012925.1:WP_004514199.1  12 HDRLKRKELSSVEATRAMLARIEAVDPKVNAYITVTPEEALAAAEAADRRIAaGDmAPLTGIPVALKDI 80 
                                               67899**********************************************975546************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               +++k+i+ttcaSkiL+n+v+pyd t v +lkeaga+i+Gk N DEFamGss+e+Safg+t+nP+n e +
  lcl|NCBI__GCF_000012925.1:WP_004514199.1  81 FVTKGIRTTCASKILDNFVPPYDGTAVAKLKEAGAVIVGKLNQDEFAMGSSGESSAFGPTRNPWNLECI 149
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSs+Gsaaa+aa ++  +lg+DTGgSiRqPAs+cg+vGl+PtYG+vSRyG++ayasSldq+G+++++
  lcl|NCBI__GCF_000012925.1:WP_004514199.1 150 PGGSSSGSAAAIAARTATATLGTDTGGSIRQPASHCGCVGLRPTYGRVSRYGVIAYASSLDQVGPVTRD 218
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekle 275
                                               v+d al+l++++g+D +Dsts+ev+v+++ + l+ d+kglk+g+ ke+  e+ld +vk+++++++e+ +
  lcl|NCBI__GCF_000012925.1:WP_004514199.1 219 VTDCALMLQAVAGHDPMDSTSVEVPVPDYAKGLTGDVKGLKLGLPKEYYIEGLDPDVKKALDEAIETYR 287
                                               ********************************************************************* PP

                                 TIGR00132 276 elgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkr 344
                                                lgae+v++slp+ ++a+a+Yy+i+++Eassnlary+g+r+G+r+e + +l +++ ktRsegfg+evkr
  lcl|NCBI__GCF_000012925.1:WP_004514199.1 288 GLGAEFVDISLPHTDYAVATYYLIATAEASSNLARYEGVRFGHRTEGAANLIDMFRKTRSEGFGDEVKR 356
                                               ********************************************************************* PP

                                 TIGR00132 345 RimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDv 413
                                               Rim+G+yals++yyd+yy+kAqkvrtli+++f k+fe vD i++p+apt afk+gek++dpl+mylsD+
  lcl|NCBI__GCF_000012925.1:WP_004514199.1 357 RIMIGTYALSSGYYDAYYLKAQKVRTLIMQDFLKAFEAVDAILTPVAPTPAFKIGEKTSDPLRMYLSDI 425
                                               ********************************************************************* PP

                                 TIGR00132 414 ltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                               +t+p+nlaG++a+svP+g++  glpiGlq+ig+ f ++++l++a+a+eqa+
  lcl|NCBI__GCF_000012925.1:WP_004514199.1 426 FTIPVNLAGTCAVSVPAGMSGAGLPIGLQLIGRPFGEETILRAAHAFEQAT 476
                                               ************************************************986 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: 00:00:00.03
# Mc/sec: 7.45
//
[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