Alignments for a candidate for gatA in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Thermodesulforhabdus norvegica DSM 9990

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_093396113.1 BM091_RS12120 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_900114975.1:WP_093396113.1
          Length = 490

 Score =  472 bits (1214), Expect = e-137
 Identities = 243/472 (51%), Positives = 339/472 (71%), Gaps = 5/472 (1%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           I EL++ I K E+  +++V  S +RI+ ++  + AF+ + EE +   A++LD+  +   +
Sbjct: 13  IHELRRHILKGEVTATEVVKASLERIREMNGLLNAFITVLEESSIEEAEKLDKNPELLKK 72

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
             L  G+P+ VKD + T+ +RTTC SKILENF P ++AT V RL++A AV +GK NMDEF
Sbjct: 73  LPL-GGVPVAVKDCLCTQKVRTTCGSKILENFCPPFNATCVSRLREAGAVIVGKTNMDEF 131

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSSTE+SAY  ++NPW+ D VPGGSSGGSA AVA+G VP +LG+DTGGSIR PA+FCG
Sbjct: 132 AMGSSTEHSAYGPSRNPWDTDRVPGGSSGGSAVAVASGMVPAALGTDTGGSIRLPAAFCG 191

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           VVGLKPTYGRVSRYGL+ FASS DQ GPITRT +D A +LQ I+G D +DSTS    V  
Sbjct: 192 VVGLKPTYGRVSRYGLIEFASSFDQAGPITRTAKDAALMLQIIAGHDPLDSTSVPEPVHS 251

Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307
           ++  L       ++ +P+EY    +  E   ++  A+ VL+ LGA + +VSLPH+ Y +A
Sbjct: 252 YVDLLEQSPFPCRVGIPREYFSYEINGEISGAIEKAMDVLKKLGAEFVDVSLPHTDYGVA 311

Query: 308 TYYLLSSSEASANLARFDGIRYGYR--TDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFA 365
            YY+++ +EAS+NLAR+DG++YG+R  TD  D L+++Y +TRA GFG EVKRRIMLGT+ 
Sbjct: 312 AYYIIAPAEASSNLARYDGVKYGFRAQTDFPD-LMEMYLKTRAVGFGKEVKRRIMLGTYV 370

Query: 366 LSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYAND 425
           LS+GYY+AYY KA +VR LI++DF   FE+ DV+  P +PT  F+IGE   +PL MY  D
Sbjct: 371 LSAGYYEAYYGKASQVRRLIQQDFLKAFEQCDVLFTPVSPTLPFRIGEKVDNPLAMYLTD 430

Query: 426 ILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQAT 476
           + T+P +LAG+PGISVPC ++  GLP+  Q++  +F E  + R+AHA+++ T
Sbjct: 431 VFTLPASLAGIPGISVPCSMSSGGLPIAFQLLAPYFREDLLLRMAHAYQKET 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: 609
Number of extensions: 28
Number of successful extensions: 4
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_093396113.1 BM091_RS12120 (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.7068.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.9e-188  610.5   0.0   1.2e-187  610.2   0.0    1.0  1  lcl|NCBI__GCF_900114975.1:WP_093396113.1  BM091_RS12120 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900114975.1:WP_093396113.1  BM091_RS12120 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 !  610.2   0.0  1.2e-187  1.2e-187       2     463 ..      17     481 ..      16     483 .. 0.98

  Alignments for each domain:
  == domain 1  score: 610.2 bits;  conditional E-value: 1.2e-187
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kek.klagipiavKd 67 
                                               ++ + k ev+++ev++++leri +++  +naf++v +e+++++a+kldk+ +  k k +l g+p+avKd
  lcl|NCBI__GCF_900114975.1:WP_093396113.1  17 RRHILKGEVTATEVVKASLERIREMNGLLNAFITVLEESSIEEAEKLDKNPEllK-KlPLGGVPVAVKD 84 
                                               6778999******************************************998644.459********** PP

                                 TIGR00132  68 niavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneer 136
                                                ++++ ++ttc+SkiLen+ +p++at v rl+eaga+i+GktN+DEFamGsste+Sa+g+ +nP++++r
  lcl|NCBI__GCF_900114975.1:WP_093396113.1  85 CLCTQKVRTTCGSKILENFCPPFNATCVSRLREAGAVIVGKTNMDEFAMGSSTEHSAYGPSRNPWDTDR 153
                                               ********************************************************************* PP

                                 TIGR00132 137 vpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilak 205
                                               vpGGSsgGsa ava ++vp alg+DTGgSiR PA+fcgvvGlKPtYG+vSRyGl+++asS+dq G++++
  lcl|NCBI__GCF_900114975.1:WP_093396113.1 154 VPGGSSGGSAVAVASGMVPAALGTDTGGSIRLPAAFCGVVGLKPTYGRVSRYGLIEFASSFDQAGPITR 222
                                               ********************************************************************* PP

                                 TIGR00132 206 kvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekl 274
                                               + +d+al+l++i+g+D  Dsts+  +v++++  l++     +vg+ +e++  +++ e++ ++ek++++l
  lcl|NCBI__GCF_900114975.1:WP_093396113.1 223 TAKDAALMLQIIAGHDPLDSTSVPEPVHSYVDLLEQSPFPCRVGIPREYFSYEINGEISGAIEKAMDVL 291
                                               ************************************9******************************** PP

                                 TIGR00132 275 eelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveel.kslkelyaktRsegfgeev 342
                                               ++lgae+v+vslp+ ++ +a+Yyii+p+Eassnlarydg++yG r++ +  +l+e+y ktR+ gfg+ev
  lcl|NCBI__GCF_900114975.1:WP_093396113.1 292 KKLGAEFVDVSLPHTDYGVAAYYIIAPAEASSNLARYDGVKYGFRAQTDfPDLMEMYLKTRAVGFGKEV 360
                                               *********************************************9865156***************** PP

                                 TIGR00132 343 krRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyls 411
                                               krRimlG+y+ls++yy++yy kA +vr+li+++f k+fe++Dv+++p++ptl+f++gek ++pl+myl+
  lcl|NCBI__GCF_900114975.1:WP_093396113.1 361 KRRIMLGTYVLSAGYYEAYYGKASQVRRLIQQDFLKAFEQCDVLFTPVSPTLPFRIGEKVDNPLAMYLT 429
                                               ********************************************************************* PP

                                 TIGR00132 412 DvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqa 463
                                               Dv+t+pa+laG+p+isvP+++++ glpi  q+ + +f ++ ll++a+a++++
  lcl|NCBI__GCF_900114975.1:WP_093396113.1 430 DVFTLPASLAGIPGISVPCSMSSGGLPIAFQLLAPYFREDLLLRMAHAYQKE 481
                                               ************************************************9987 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: 00:00:00.03
# Mc/sec: 7.22
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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