Alignments for a candidate for gatA in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Thiomicrospira cyclica ALM1

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013835792.1 THICY_RS06345 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000214825.1:WP_013835792.1
          Length = 488

 Score =  473 bits (1217), Expect = e-138
 Identities = 234/472 (49%), Positives = 325/472 (68%), Gaps = 1/472 (0%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           + EL Q +  K+I   +L +    RI A + ++ +F+    E+A   A+  D+ +  + +
Sbjct: 6   LAELNQALQSKQISSVELTEFFLARIAAHEPELNSFITTTPEQALRMAQAADQRL-AKGD 64

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
              L G+P+  KD   T G+ TTC SK+L NF   YDA +V + +  +   +GK NMDEF
Sbjct: 65  APNLCGIPMAHKDIFCTDGVLTTCGSKMLANFTAPYDAHIVSQFKALDMPVLGKTNMDEF 124

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS E+S +   KNPW+LD VPGGSSGGSAAAVAAG  PF+ GSDTGGSIRQPASFCG
Sbjct: 125 AMGSSNESSFFGAVKNPWSLDRVPGGSSGGSAAAVAAGLTPFATGSDTGGSIRQPASFCG 184

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           + GLKPTYG  SR+G++A+ASS DQ GP+ ++ +D A  L  +   D  DSTS +   PD
Sbjct: 185 ISGLKPTYGLASRFGMIAYASSFDQAGPMAQSAQDLALTLDVMHSFDLRDSTSLDQPKPD 244

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           ++++L   + GL+I VP  Y GEG+  + ++ +  A+   E LGA    V LP+  +A+A
Sbjct: 245 YVAALAQPLAGLRIGVPTSYFGEGLDADVKKVIETAIAEYEKLGAELVAVELPNQAHAVA 304

Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367
            YY+L+ +EAS+NL+RFDG+RYG+R ++  +L DLY ++RAEGFG EV++RIMLG +ALS
Sbjct: 305 AYYILAPAEASSNLSRFDGVRYGHRCEDPKDLADLYGRSRAEGFGIEVQKRIMLGAYALS 364

Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427
           +GYYDAYY KAQKVR LI++DF   FE+ DVI+GP  PTPAFK+GE + DPL+MY  D+ 
Sbjct: 365 AGYYDAYYLKAQKVRRLIQQDFLSAFEQCDVIMGPVAPTPAFKLGEKSDDPLSMYLADLY 424

Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHH 479
           TIPVNLAG+P +S+P G   G+P+GL ++G +F E+ +  VAH ++  TD H
Sbjct: 425 TIPVNLAGLPAMSLPAGQVKGMPVGLHLVGPYFSEAKLLNVAHQYQLHTDWH 476


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: 559
Number of extensions: 22
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: 488
Length adjustment: 34
Effective length of query: 451
Effective length of database: 454
Effective search space:   204754
Effective search space used:   204754
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_013835792.1 THICY_RS06345 (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.1090354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-182  592.4   0.0   3.4e-182  592.3   0.0    1.0  1  NCBI__GCF_000214825.1:WP_013835792.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214825.1:WP_013835792.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.3   0.0  3.4e-182  3.4e-182       2     463 ..      10     472 ..       9     475 .. 0.98

  Alignments for each domain:
  == domain 1  score: 592.3 bits;  conditional E-value: 3.4e-182
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.kek.klagipiavKdniavk 72 
                                           +++l++k++s++e++e +l+ri a++ ++n+f+++t+e+al++a++ d+++a  +  +l gip+a Kd +++ 
  NCBI__GCF_000214825.1:WP_013835792.1  10 NQALQSKQISSVELTEFFLARIAAHEPELNSFITTTPEQALRMAQAADQRLAkGDApNLCGIPMAHKDIFCTD 82 
                                           68899**********************************************9544459*************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145
                                           ++ ttc+Sk+L n+++pyda++v + k+ ++ ++GktN+DEFamGss e+S+fg++knP+  +rvpGGSsgGs
  NCBI__GCF_000214825.1:WP_013835792.1  83 GVLTTCGSKMLANFTAPYDAHIVSQFKALDMPVLGKTNMDEFAMGSSNESSFFGAVKNPWSLDRVPGGSSGGS 155
                                           ************************************************************************* PP

                             TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218
                                           aaavaa+l p+a gsDTGgSiRqPAsfcg+ GlKPtYGl SR+G++ayasS+dq G++a++ +d+al ldv++
  NCBI__GCF_000214825.1:WP_013835792.1 156 AAAVAAGLTPFATGSDTGGSIRQPASFCGISGLKPTYGLASRFGMIAYASSFDQAGPMAQSAQDLALTLDVMH 228
                                           ************************************************************************* PP

                             TIGR00132 219 gkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvkl 291
                                             D +Dstsl+ ++++++ +l++ l gl++gv   +++e+ld +vk+ +e+++ + e+lgae+v v+lp+   
  NCBI__GCF_000214825.1:WP_013835792.1 229 SFDLRDSTSLDQPKPDYVAALAQPLAGLRIGVPTSYFGEGLDADVKKVIETAIAEYEKLGAELVAVELPNQAH 301
                                           ************************************************************************* PP

                             TIGR00132 292 alaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364
                                           a+a+Yyi++p+Eassnl+r+dg+ryG+r e++k+l +ly ++R+egfg ev++RimlGayals++yyd+yy+k
  NCBI__GCF_000214825.1:WP_013835792.1 302 AVAAYYILAPAEASSNLSRFDGVRYGHRCEDPKDLADLYGRSRAEGFGIEVQKRIMLGAYALSAGYYDAYYLK 374
                                           ************************************************************************* PP

                             TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekgl 437
                                           Aqkvr+li+++f  +fe++Dvi++p+apt afklgek +dpl+myl+D++t+p+nlaGlpa+s+P+g+  kg+
  NCBI__GCF_000214825.1:WP_013835792.1 375 AQKVRRLIQQDFLSAFEQCDVIMGPVAPTPAFKLGEKSDDPLSMYLADLYTIPVNLAGLPAMSLPAGQV-KGM 446
                                           *********************************************************************.8** PP

                             TIGR00132 438 piGlqiigkafddkkllsvakaleqa 463
                                           p+Gl ++g +f++ kll+va++++ +
  NCBI__GCF_000214825.1:WP_013835792.1 447 PVGLHLVGPYFSEAKLLNVAHQYQLH 472
                                           ********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (488 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.62
//
[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