Alignments for a candidate for gatA in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Methylovulum miyakonense HT12

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_019865464.1 METMI_RS0106505 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000384075.1:WP_019865464.1
          Length = 481

 Score =  486 bits (1251), Expect = e-142
 Identities = 245/478 (51%), Positives = 329/478 (68%), Gaps = 2/478 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I +L Q +   E    +L     +RI+   + + AF+ + E  A   A+  D+ +    +
Sbjct: 6   INQLAQGLRSGEFSSVELTQHFLQRIRQ-HESLNAFITVTEGLALQAAQAADQRI-ASGD 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             LL G+PI  KD   T G++T+C SK+L+NF   Y+ATVV++   A AV +GKLNMDEF
Sbjct: 64  ASLLAGIPIAQKDIFCTLGVKTSCGSKMLDNFIAPYNATVVEKFNHAGAVMLGKLNMDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS E S Y   +NPW+  TVPGGSSGGSAAAVAAG    + G+DTGGSIRQPA+FCG
Sbjct: 124 AMGSSNETSFYGPARNPWDTQTVPGGSSGGSAAAVAAGLAVAATGTDTGGSIRQPAAFCG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + GLKPTYGRVSRYG++A+ASSLDQ GP+TRT ED A LLQ ++G D  DSTSA++ VPD
Sbjct: 184 ITGLKPTYGRVSRYGMIAYASSLDQGGPMTRTAEDAAILLQTMAGFDAKDSTSADLPVPD 243

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           + ++L   + GLKI +PKE+ GEG+       +  A+     LGA   ++S+P+   A+ 
Sbjct: 244 YPAALNQPLAGLKIGLPKEFFGEGLDSGVAAVLETAISEYRKLGAEVADISMPNLNMAIP 303

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+++ +E+SANL+R+DG+R+GYR ++  +L DLY ++R EGFG EVKRRI++GT+ALS
Sbjct: 304 AYYVIACAESSANLSRYDGVRFGYRCESPVDLTDLYTRSRGEGFGKEVKRRILMGTYALS 363

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQKVR LI +DF+    + DVI+ P TPT AF IG    DP+ MY  DI 
Sbjct: 364 AGYYDAYYLKAQKVRRLISQDFQQALAQVDVIMSPVTPTTAFGIGAKMDDPIAMYLADIY 423

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485
           TI +NLAGVP +SVP G + G+P+GLQIIG HF E  +  +AH ++Q TD H+  P L
Sbjct: 424 TIAINLAGVPAMSVPAGFSGGMPVGLQIIGNHFTEDRLLNIAHQYQQVTDWHQQTPTL 481


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: 28
Number of successful extensions: 1
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: 481
Length adjustment: 34
Effective length of query: 451
Effective length of database: 447
Effective search space:   201597
Effective search space used:   201597
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_019865464.1 METMI_RS0106505 (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.1933833.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-187  609.7   0.0     2e-187  609.5   0.0    1.0  1  NCBI__GCF_000384075.1:WP_019865464.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000384075.1:WP_019865464.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.5   0.0    2e-187    2e-187       5     465 ..      13     473 ..       9     474 .. 0.98

  Alignments for each domain:
  == domain 1  score: 609.5 bits;  conditional E-value: 2e-187
                             TIGR00132   5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdie 75 
                                           l + e+s++e+++++l+ri ++++ +naf++vt+  al++a++ d+++a  + ++lagipia Kd +++ +++
  NCBI__GCF_000384075.1:WP_019865464.1  13 LRSGEFSSVELTQHFLQRIRQHES-LNAFITVTEGLALQAAQAADQRIAsGDaSLLAGIPIAQKDIFCTLGVK 84 
                                           66778999***************9.***********************974547******************* PP

                             TIGR00132  76 ttcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaa 148
                                           t+c+Sk+L+n+++py+atVve+ ++aga+++Gk N+DEFamGss etS++g+ +nP+++++vpGGSsgGsaaa
  NCBI__GCF_000384075.1:WP_019865464.1  85 TSCGSKMLDNFIAPYNATVVEKFNHAGAVMLGKLNMDEFAMGSSNETSFYGPARNPWDTQTVPGGSSGGSAAA 157
                                           ************************************************************************* PP

                             TIGR00132 149 vaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkD 221
                                           vaa+l++ a g+DTGgSiRqPA+fcg+ GlKPtYG+vSRyG++ayasSldq G+++++ ed+a++l++++g D
  NCBI__GCF_000384075.1:WP_019865464.1 158 VAAGLAVAATGTDTGGSIRQPAAFCGITGLKPTYGRVSRYGMIAYASSLDQGGPMTRTAEDAAILLQTMAGFD 230
                                           ************************************************************************* PP

                             TIGR00132 222 kkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklala 294
                                           +kDsts++ +v+++  +l++ l glk+g+ ke+++e+ld++v++ +e+++ + ++lgae+ ++s+p++++a++
  NCBI__GCF_000384075.1:WP_019865464.1 231 AKDSTSADLPVPDYPAALNQPLAGLKIGLPKEFFGEGLDSGVAAVLETAISEYRKLGAEVADISMPNLNMAIP 303
                                           ************************************************************************* PP

                             TIGR00132 295 iYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqk 367
                                           +Yy+i+ +E s+nl+rydg+r+G+r e + +l++ly+++R egfg+evkrRi++G+yals++yyd+yy+kAqk
  NCBI__GCF_000384075.1:WP_019865464.1 304 AYYVIACAESSANLSRYDGVRFGYRCESPVDLTDLYTRSRGEGFGKEVKRRILMGTYALSAGYYDAYYLKAQK 376
                                           ************************************************************************* PP

                             TIGR00132 368 vrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiG 440
                                           vr+li ++f++++ +vDvi+sp++pt+af +g+k++dp++myl+D++t+ +nlaG+pa+svP+g +  g+p+G
  NCBI__GCF_000384075.1:WP_019865464.1 377 VRRLISQDFQQALAQVDVIMSPVTPTTAFGIGAKMDDPIAMYLADIYTIAINLAGVPAMSVPAGFS-GGMPVG 448
                                           ******************************************************************.6***** PP

                             TIGR00132 441 lqiigkafddkkllsvakaleqald 465
                                           lqiig++f +++ll++a++++q +d
  NCBI__GCF_000384075.1:WP_019865464.1 449 LQIIGNHFTEDRLLNIAHQYQQVTD 473
                                           ********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (481 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: 17.84
//
[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