Alignments for a candidate for gatB in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Persephonella marina EX-H1

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012675967.1 PERMA_RS02770 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000021565.1:WP_012675967.1
          Length = 474

 Score =  517 bits (1332), Expect = e-151
 Identities = 256/473 (54%), Positives = 345/473 (72%), Gaps = 1/473 (0%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M FE VIGLEVHV++ T++K F      FGAEPN+N   + L  PG LPV+NK+A+++A+
Sbjct: 1   MEFEPVIGLEVHVQMSTNTKCFCSCKIEFGAEPNTNVCPVCLGMPGSLPVLNKKALEYAI 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITR 120
           +A++ALN E+   S F RKNYFYPD PK YQISQ+D+P+  NGYIDI+V+ +T+RI I R
Sbjct: 61  KASLALNCEVHELSVFARKNYFYPDLPKGYQISQYDKPLATNGYIDIKVNDKTERIRIHR 120

Query: 121 LHMEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180
           LHMEEDAGK+ HKG YS VDLNR GTPL+EIVSEPDIRS   A  YLEKLR+I++Y GVS
Sbjct: 121 LHMEEDAGKTIHKGSYSYVDLNRAGTPLMEIVSEPDIRSAVGARLYLEKLRNIMRYIGVS 180

Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240
           D  ME+G LRCD NISLRP G+EKFGTK E+KN+NSF +V+K +EYE +RQ   L  GGE
Sbjct: 181 DADMEKGQLRCDVNISLRPKGEEKFGTKVEIKNINSFRFVQKAIEYEIERQARILRKGGE 240

Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300
           I QETR FDE TGKT  MR KE + DYRYFP+PD++P+ I   + E +R+++PELPD++ 
Sbjct: 241 IVQETRLFDEKTGKTFTMRTKEEAHDYRYFPDPDLIPVRITKEYIEEIRKSLPELPDQKA 300

Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIE-HGADVKLTSNWLMGGVNEYLNKNQVEL 359
            +YV EL L  YDA VL   K+ + FFE  +  +  + K  +NW++  +   LN+  +E+
Sbjct: 301 ERYVKELKLTEYDAEVLVADKDRALFFEKAVSVYSENPKSIANWIINELLGKLNEEGIEI 360

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419
            ++ + PE++A +++LI+ G +SSKI K+VF E+   G + K I+E+ GL Q+SDE  + 
Sbjct: 361 SNSPVRPEHIAELVQLIDKGDISSKIGKEVFEEVFKTGKSPKTIVEEKGLKQVSDEGEIR 420

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
           K V E L+N+   VE YK G  K MGF VGQ+MKA++G+ANP+LVN++L++ L
Sbjct: 421 KIVEEVLNNHPAEVEKYKAGNQKLMGFFVGQVMKATRGKANPKLVNKILQELL 473


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: 664
Number of extensions: 24
Number of successful extensions: 2
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: 474
Length adjustment: 33
Effective length of query: 442
Effective length of database: 441
Effective search space:   194922
Effective search space used:   194922
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: 51 (24.3 bits)

Align candidate WP_012675967.1 PERMA_RS02770 (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.3614067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-199  648.9   3.4   2.4e-199  648.7   3.4    1.0  1  NCBI__GCF_000021565.1:WP_012675967.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021565.1:WP_012675967.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.7   3.4  2.4e-199  2.4e-199       2     480 ..       1     473 [.       1     474 [] 0.99

  Alignments for each domain:
  == domain 1  score: 648.7 bits;  conditional E-value: 2.4e-199
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +e+e viGlEvHvq+ t++K Fc+c+ e+   +pNtnvcpvclg+PG+lPvlNk+a++ A+k +laln++ v+
  NCBI__GCF_000021565.1:WP_012675967.1   1 MEFEPVIGLEVHVQMSTNTKCFCSCKIEFGA-EPNTNVCPVCLGMPGSLPVLNKKALEYAIKASLALNCE-VH 71 
                                           68999************************99.**************************************.66 PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkdkqslvD 147
                                           e svF+RK+YfYpDlPkgyqi+q+d+P+a++G+++i++++k  +i+i+rlh+EeD+gk+ +k+s    +s+vD
  NCBI__GCF_000021565.1:WP_012675967.1  72 ELSVFARKNYFYPDLPKGYQISQYDKPLATNGYIDIKVNDKTERIRIHRLHMEEDAGKTIHKGS----YSYVD 140
                                           8*************************************************************66....9**** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                           +NR+g+PL+EiV++Pd++sa  ar +l+klr+i+ry+++sd+d+e+G +R+DvN+s+r+kG+ek+gt+vEiKN
  NCBI__GCF_000021565.1:WP_012675967.1 141 LNRAGTPLMEIVSEPDIRSAVGARLYLEKLRNIMRYIGVSDADMEKGQLRCDVNISLRPKGEEKFGTKVEIKN 213
                                           ************************************************************************* PP

                             TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvk 293
                                           +ns++ ++kaieyEieRq ++l+kg e++qetr fdek+ +t ++R Kee++DYRYfp+Pdl p+ i++e+++
  NCBI__GCF_000021565.1:WP_012675967.1 214 INSFRFVQKAIEYEIERQARILRKGGEIVQETRLFDEKTGKTFTMRTKEEAHDYRYFPDPDLIPVRITKEYIE 286
                                           ************************************************************************* PP

                             TIGR00133 294 ekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep.klavnWileellgeLnkkki 365
                                           e +++ lpelP++k +r++ke++l e+da+vlv+d++ +  fe++v++ +e+ k  +nWi++ellg+Ln++ i
  NCBI__GCF_000021565.1:WP_012675967.1 287 E-IRKSLPELPDQKAERYVKELKLTEYDAEVLVADKDRALFFEKAVSVYSENpKSIANWIINELLGKLNEEGI 358
                                           *.*******************************************99987765999***************** PP

                             TIGR00133 366 slaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenp 438
                                           +++++ ++pe++ael++li++g is+k++ke++ee+++++k+pk+++e++gl q+sde e+ kiveev++++p
  NCBI__GCF_000021565.1:WP_012675967.1 359 EISNSPVRPEHIAELVQLIDKGDISSKIGKEVFEEVFKTGKSPKTIVEEKGLKQVSDEGEIRKIVEEVLNNHP 431
                                           ************************************************************************* PP

                             TIGR00133 439 kevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            evekyk+g +k+++f+vGqvmk t+g+a+pk v+k+l+ell
  NCBI__GCF_000021565.1:WP_012675967.1 432 AEVEKYKAGNQKLMGFFVGQVMKATRGKANPKLVNKILQELL 473
                                           ****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (474 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: 15.05
//
[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