Alignments for a candidate for gatA in Sulfuritalea hydrogenivorans DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Sulfuritalea hydrogenivorans DSM 22779

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_041096420.1 SUTH_RS01140 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000828635.1:WP_041096420.1
          Length = 490

 Score =  469 bits (1208), Expect = e-137
 Identities = 239/484 (49%), Positives = 328/484 (67%), Gaps = 2/484 (0%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           L +  + EL   +  K++   +L      RI+  +  + AF+ LD ++  A A+  D  V
Sbjct: 4   LINSSLRELSAALAAKKVSAVELASLFLDRIETFNPALNAFITLDRDKTLAQARAADAKV 63

Query: 63  D-GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGK 121
             G + +  L G+P+  KD   T+G RT+C S++L NF   YDA VV++L  A  VT+GK
Sbjct: 64  GAGGTANSPLCGIPLAHKDIFCTQGWRTSCGSQMLANFVSPYDANVVEKLAAAGMVTLGK 123

Query: 122 LNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQ 181
           LNMDEFAMGSS E S +   KNPW++  VPGGSSGGSAAA+AA   P + G+DTGGSIRQ
Sbjct: 124 LNMDEFAMGSSNETSYFGPVKNPWDVSRVPGGSSGGSAAAIAARLTPAATGTDTGGSIRQ 183

Query: 182 PASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSA 241
           PA+ CG+ GLKPTYG VSRYG++AFASSLDQ GP+ ++ +D A LL A++G D  DSTS 
Sbjct: 184 PAALCGLTGLKPTYGVVSRYGMIAFASSLDQGGPMAKSADDCALLLNAMAGFDPRDSTSL 243

Query: 242 NVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPH 301
                D+   L   + GL+I +P+E+ G+G+  + R +V AAL     LGAT  EV LP+
Sbjct: 244 ERPAEDYGRDLEKPLAGLRIGLPREFFGDGMDADVRAAVEAALAEYRKLGATTVEVQLPN 303

Query: 302 SKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIML 361
           S  ++  YY+++ +EAS+NL+RFDG+RYGYR    D+L ++Y ++RA+GFG EVKRRI++
Sbjct: 304 SGLSVPAYYVIAPAEASSNLSRFDGVRYGYRAPEYDDLTEMYSRSRAQGFGAEVKRRILI 363

Query: 362 GTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTM 421
           GT+ LS GYYDAYY KAQK+R LI  DF + F+  DVI+GPT+P+ AF  G  + DP+ M
Sbjct: 364 GTYVLSHGYYDAYYLKAQKIRRLIAADFVEAFKACDVIMGPTSPSVAFAFGAKSADPVQM 423

Query: 422 YANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHK 480
           Y +DI TI  NLAG+PG+S+PCG  A+ +P+GLQIIG    E+ +  VAH +++ATD H 
Sbjct: 424 YLSDIYTISTNLAGLPGMSLPCGFGANNMPVGLQIIGNWLGEAKMLNVAHQYQKATDWHT 483

Query: 481 AKPE 484
             PE
Sbjct: 484 RMPE 487


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: 565
Number of extensions: 20
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: 490
Length adjustment: 34
Effective length of query: 451
Effective length of database: 456
Effective search space:   205656
Effective search space used:   205656
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_041096420.1 SUTH_RS01140 (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.3134.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-184  600.1   0.0   1.7e-184  599.9   0.0    1.0  1  lcl|NCBI__GCF_000828635.1:WP_041096420.1  SUTH_RS01140 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041096420.1  SUTH_RS01140 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 !  599.9   0.0  1.7e-184  1.7e-184       3     465 ..      14     480 ..      12     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 599.9 bits;  conditional E-value: 1.7e-184
                                 TIGR00132   3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva...ke.kklagipiavKd 67 
                                               ++l +k+vs++e+++ +l+rie+++  +naf++++++k+l++a++ d+kv    +  ++l gip+a Kd
  lcl|NCBI__GCF_000828635.1:WP_041096420.1  14 AALAAKKVSAVELASLFLDRIETFNPALNAFITLDRDKTLAQARAADAKVGaggTAnSPLCGIPLAHKD 82 
                                               67889********************************************988853336*********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                                +++++++t+c+S++L n+vspyda Vve+l +ag++++Gk N+DEFamGss etS+fg++knP++ +r
  lcl|NCBI__GCF_000828635.1:WP_041096420.1  83 IFCTQGWRTSCGSQMLANFVSPYDANVVEKLAAAGMVTLGKLNMDEFAMGSSNETSYFGPVKNPWDVSR 151
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsaaa+aa l p a g+DTGgSiRqPA++cg  GlKPtYG+vSRyG++a+asSldq G++ak
  lcl|NCBI__GCF_000828635.1:WP_041096420.1 152 VPGGSSGGSAAAIAARLTPAATGTDTGGSIRQPAALCGLTGLKPTYGVVSRYGMIAFASSLDQGGPMAK 220
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               + +d al+l++++g D +Dstsle + e++ ++l+k l gl++g+ +e++++++d +v++++e++l + 
  lcl|NCBI__GCF_000828635.1:WP_041096420.1 221 SADDCALLLNAMAGFDPRDSTSLERPAEDYGRDLEKPLAGLRIGLPREFFGDGMDADVRAAVEAALAEY 289
                                               ********************************************************************* PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevk 343
                                               ++lga+ vev+lp++ l++++Yy+i+p+Eassnl+r+dg+ryG+r+ e+++l+e+y+++R++gfg+evk
  lcl|NCBI__GCF_000828635.1:WP_041096420.1 290 RKLGATTVEVQLPNSGLSVPAYYVIAPAEASSNLSRFDGVRYGYRAPEYDDLTEMYSRSRAQGFGAEVK 358
                                               ********************************************************************* PP

                                 TIGR00132 344 rRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsD 412
                                               rRi++G+y+ls++yyd+yy+kAqk+r+li+ +f ++f+ +Dvi++pt+p +af +g+k +dp++mylsD
  lcl|NCBI__GCF_000828635.1:WP_041096420.1 359 RRILIGTYVLSHGYYDAYYLKAQKIRRLIAADFVEAFKACDVIMGPTSPSVAFAFGAKSADPVQMYLSD 427
                                               ********************************************************************* PP

                                 TIGR00132 413 vltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               ++t+  nlaGlp++s+P+g   +++p+Glqiig+ + + k+l+va+++++a+d
  lcl|NCBI__GCF_000828635.1:WP_041096420.1 428 IYTISTNLAGLPGMSLPCGFGANNMPVGLQIIGNWLGEAKMLNVAHQYQKATD 480
                                               ************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (490 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: 7.74
//
[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