Alignments for a candidate for gatB in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Haloechinothrix alba DSM 45207

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_281251727.1 CHB84_RS03185 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_900188115.1:WP_281251727.1
          Length = 502

 Score =  396 bits (1018), Expect = e-115
 Identities = 217/482 (45%), Positives = 301/482 (62%), Gaps = 15/482 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           F+ V+GLEVHVEL T +KMF   P  FG EPN++     L  PG LPVVN  AV+ A+R 
Sbjct: 17  FDPVLGLEVHVELSTRTKMFCGCPNAFGGEPNTHVCPTCLGLPGALPVVNGSAVESAIRI 76

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            + LN EIA   +F RKNYFYPD PK +Q SQ+D+PI  +GY+D+E+ DGET R+GI R 
Sbjct: 77  GLGLNCEIAGWCRFARKNYFYPDMPKNFQTSQYDEPIAFDGYLDVELGDGETVRVGIERA 136

Query: 122 HMEEDAGKSTHKG---------EYSLVDLNRQGTPLIEIVSEPDI----RSPKEAYAYLE 168
           HMEED GKS H G         +YSL+D NR G PLIEIV++P      R+P+ A AY+ 
Sbjct: 137 HMEEDTGKSLHVGGATGRIHGADYSLLDYNRAGVPLIEIVTKPITGAGRRAPEVARAYVT 196

Query: 169 KLRSIIQYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEE 228
            LR +++  GVSDV+M++GSLRCDAN+SL P G E FGT++E KN+NS   V + + YE 
Sbjct: 197 ALRDLLRAMGVSDVRMDQGSLRCDANVSLSPKGDEAFGTRSETKNVNSLRSVERAVRYEM 256

Query: 229 KRQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERV 288
            RQ   L  G  + QETR F E+ G T   R KE S+DYRYFPEPD+VP+    AW E +
Sbjct: 257 TRQATLLSRGERVVQETRHFQEADGTTSAGRPKETSEDYRYFPEPDLVPIAPSSAWVEEL 316

Query: 289 RQTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGV 348
           R T+PELP ER+ +   E  L   +   L  T   +D   +T++ GA V    +W +  +
Sbjct: 317 RSTLPELPWERRRRIQQEWQLTDEELRDLVNT-GAADVVAATVDAGAPVDDARSWWVQFL 375

Query: 349 NEYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNG 408
            E  N   V+L D  +TP  +A +I LI +GT+++K+ ++V   + A  G+  +++   G
Sbjct: 376 TEQANSRGVDLADLPVTPAQVARVIALISEGTLTNKLGREVVLGVLAGEGDPDEVIASRG 435

Query: 409 LVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLL 468
           L  +SD++ L   ++EAL      VE  + GK +A G +VG +MKA++GQA+ + V +L+
Sbjct: 436 LEVVSDDSALTAAIDEALAAQPDVVEKIRGGKVQAAGAIVGAVMKATQGQADAKRVRELI 495

Query: 469 KQ 470
            Q
Sbjct: 496 LQ 497


Lambda     K      H
   0.313    0.133    0.373 

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: 621
Number of extensions: 26
Number of successful extensions: 5
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: 475
Length of database: 502
Length adjustment: 34
Effective length of query: 441
Effective length of database: 468
Effective search space:   206388
Effective search space used:   206388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate WP_281251727.1 CHB84_RS03185 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.1097031.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-149  482.6   0.0     7e-149  482.3   0.0    1.0  1  NCBI__GCF_900188115.1:WP_281251727.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900188115.1:WP_281251727.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.3   0.0    7e-149    7e-149       4     478 ..      17     497 ..      14     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 482.3 bits;  conditional E-value: 7e-149
                             TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                           ++ v+GlEvHv l t++K+Fc c+n +   +pNt+vcp clglPGalPv+N +av++A+ ++l ln++ ++  
  NCBI__GCF_900188115.1:WP_281251727.1  17 FDPVLGLEVHVELSTRTKMFCGCPNAFGG-EPNTHVCPTCLGLPGALPVVNGSAVESAIRIGLGLNCE-IAGW 87 
                                           77899************************.**************************************.557* PP

                             TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdk.....dkq 143
                                             F+RK+YfYpD+Pk++q +q+d Pia dG+l++el ++e  ++gier h+EeDtgks + +  +     +++
  NCBI__GCF_900188115.1:WP_281251727.1  88 CRFARKNYFYPDMPKNFQTSQYDEPIAFDGYLDVELGDGEtVRVGIERAHMEEDTGKSLHVGGATgrihgADY 160
                                           ***********************************98877589*****************987766687899* PP

                             TIGR00133 144 slvDfNRsgvPLlEiVtkPdl....ksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqeke 212
                                           sl+D+NR+gvPL+EiVtkP      + ++ ara++  lr +lr +++sd  +++Gs+R+D+Nvs+ +kG+e++
  NCBI__GCF_900188115.1:WP_281251727.1 161 SLLDYNRAGVPLIEIVTKPITgagrRAPEVARAYVTALRDLLRAMGVSDVRMDQGSLRCDANVSLSPKGDEAF 233
                                           *******************973333567889****************************************** PP

                             TIGR00133 213 gtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppi 285
                                           gtr E KN+nsl+s+e+a+ yE++Rq  ll++ge v+qetr+f+e+  +t + R Ke+seDYRYfpePdl+pi
  NCBI__GCF_900188115.1:WP_281251727.1 234 GTRSETKNVNSLRSVERAVRYEMTRQATLLSRGERVVQETRHFQEADGTTSAGRPKETSEDYRYFPEPDLVPI 306
                                           ************************************************************************* PP

                             TIGR00133 286 eideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellg 358
                                             +  +v+e ++ +lpelP ++r r+++e +l +e+ + lv+ +  +d+    v + ++ ++a +W ++ l+ 
  NCBI__GCF_900188115.1:WP_281251727.1 307 APSSAWVEE-LRSTLPELPWERRRRIQQEWQLTDEELRDLVN-TGAADVVAATVDAGAPVDDARSWWVQFLTE 377
                                           ********9.*****************************995.678999999********************* PP

                             TIGR00133 359 eLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkive 431
                                           + n++ ++la+  ++p ++a++i+li+eg++++k ++e++  +l  ++dp+++i  +gl+ +sd+++l+++++
  NCBI__GCF_900188115.1:WP_281251727.1 378 QANSRGVDLADLPVTPAQVARVIALISEGTLTNKLGREVVLGVLAGEGDPDEVIASRGLEVVSDDSALTAAID 450
                                           ************************************************************************* PP

                             TIGR00133 432 evikenpkevekyksgkekalkflvGqvmkktkgradpkevekllke 478
                                           e+++ +p+ vek + gk +a + +vG vmk t+g+ad+k+v +l+ +
  NCBI__GCF_900188115.1:WP_281251727.1 451 EALAAQPDVVEKIRGGKVQAAGAIVGAVMKATQGQADAKRVRELILQ 497
                                           ******************************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (502 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.35
//
[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