Alignments for a candidate for gatB in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Phyllobacterium endophyticum PEPV15

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_106716492.1 CU100_RS10285 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_003010935.1:WP_106716492.1
          Length = 500

 Score =  411 bits (1056), Expect = e-119
 Identities = 213/478 (44%), Positives = 318/478 (66%), Gaps = 11/478 (2%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E V+G+EVH ++ ++SK+FS +   FGAEPN N +++D A PG+LPV+N+  V  A+R 
Sbjct: 22  WEIVVGMEVHAQVTSNSKLFSGASTTFGAEPNENVSLVDAAMPGMLPVINEWCVRQAIRT 81

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETK------RI 116
            + L  +I  +S FDRKNYFYPD P+ YQISQF QPI   G + I V  + K       I
Sbjct: 82  GLGLKAQINLKSIFDRKNYFYPDLPQGYQISQFKQPIVGEGKMIISVGPDKKGEFEDIEI 141

Query: 117 GITRLHMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSII 174
           GI RLH+E+DAGKS H      S VDLNR G  L+EIVS+PD+RS  EA AYL KLR+I+
Sbjct: 142 GIERLHLEQDAGKSLHDQNPTMSYVDLNRSGVALMEIVSKPDMRSSDEAKAYLTKLRTIV 201

Query: 175 QYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEE 234
           +Y G  D  M+EGS+R D N+S+R  G E FGT+ E+KN+NS  +V + +EYE +RQ   
Sbjct: 202 RYLGTCDGNMDEGSMRADVNVSVRKPGGE-FGTRCEIKNVNSIRFVGQAIEYEARRQIAI 260

Query: 235 LLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPE 294
           L  GG I QETR FD   G+T  MR KE + DYRYFP+PD++PL  + A+ + ++  +PE
Sbjct: 261 LEDGGSIDQETRLFDPVKGETRSMRSKEEAHDYRYFPDPDLLPLEFEQAYVDELKADLPE 320

Query: 295 LPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNK 354
           LPD++K + V+ LGL  YDA +L   K ++D++E+ +  G D KL++NW++  +   LNK
Sbjct: 321 LPDDKKLRLVSMLGLSVYDASILVTEKAIADYYEA-VAKGRDGKLSANWVINDLLGALNK 379

Query: 355 NQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISD 414
               + ++ ++PE L  +I LI++GT+S KIAK +F  + ++GG+ ++++E  G+ Q++D
Sbjct: 380 AGKGIEESPVSPEQLGAVIDLIKEGTISGKIAKDLFEIVWSEGGDPRELVESRGMKQVTD 439

Query: 415 EATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
              + K +++ +  N   VE  K  K    G+ VGQ+MK++ G+ANPQ+++ ++K +L
Sbjct: 440 TGAIEKAIDDVIAANPDKVEQAK-AKPSLAGWFVGQVMKSTGGKANPQVLSDMVKSKL 496


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: 689
Number of extensions: 30
Number of successful extensions: 6
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: 500
Length adjustment: 34
Effective length of query: 441
Effective length of database: 466
Effective search space:   205506
Effective search space used:   205506
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_106716492.1 CU100_RS10285 (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.1217054.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-165  534.6   0.0   1.1e-164  534.5   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106716492.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106716492.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.5   0.0  1.1e-164  1.1e-164       3     480 ..      21     496 ..      19     497 .. 0.97

  Alignments for each domain:
  == domain 1  score: 534.5 bits;  conditional E-value: 1.1e-164
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++e+v+G+EvH q+  +sKlF+ +s+ +   +pN+nv+ v+ ++PG lPv+N+  v++A+  +l l+++i+  
  NCBI__GCF_003010935.1:WP_106716492.1  21 DWEIVVGMEVHAQVTSNSKLFSGASTTFGA-EPNENVSLVDAAMPGMLPVINEWCVRQAIRTGLGLKAQIN-L 91 
                                           5799************************99.**************************************77.5 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke......keigierlhlEeDtgksqykesdkdk 142
                                           +s+FdRK+YfYpDlP+gyqi+q+++Pi+ +Gk+ i++  ++       eigierlhlE+D+gks + ++  ++
  NCBI__GCF_003010935.1:WP_106716492.1  92 KSIFDRKNYFYPDLPQGYQISQFKQPIVGEGKMIISVGPDKkgefedIEIGIERLHLEQDAGKSLHDQN--PT 162
                                           9**********************************99877767777779*****************955..79 PP

                             TIGR00133 143 qslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtr 215
                                           +s+vD+NRsgv L+EiV+kPd++s++ea+a+l klr+i+ryl+  dg+++eGsmR+DvNvs+r k   ++gtr
  NCBI__GCF_003010935.1:WP_106716492.1 163 MSYVDLNRSGVALMEIVSKPDMRSSDEAKAYLTKLRTIVRYLGTCDGNMDEGSMRADVNVSVR-KPGGEFGTR 234
                                           ***************************************************************.66788**** PP

                             TIGR00133 216 vEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieid 288
                                            EiKN+ns++ + +aieyE  Rq+++l++g ++ qetr fd  k  t s+R+Kee++DYRYfp+Pdl p+e++
  NCBI__GCF_003010935.1:WP_106716492.1 235 CEIKNVNSIRFVGQAIEYEARRQIAILEDGGSIDQETRLFDPVKGETRSMRSKEEAHDYRYFPDPDLLPLEFE 307
                                           ************************************************************************* PP

                             TIGR00133 289 eevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLn 361
                                           + +v+e +++ lpelP+ k+ rl++ +gls +da +lv+++ ++d++e v+k  +  kl++nW++++llg Ln
  NCBI__GCF_003010935.1:WP_106716492.1 308 QAYVDE-LKADLPELPDDKKLRLVSMLGLSVYDASILVTEKAIADYYEAVAKGRDG-KLSANWVINDLLGALN 378
                                           ******.*****************************************99997776.**************** PP

                             TIGR00133 362 kkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevi 434
                                           k    ++e+ ++pe+l ++i+likeg+is+k+ak+l+e + ++++dp++l+e +g+ q++d+ ++ k++++vi
  NCBI__GCF_003010935.1:WP_106716492.1 379 KAGKGIEESPVSPEQLGAVIDLIKEGTISGKIAKDLFEIVWSEGGDPRELVESRGMKQVTDTGAIEKAIDDVI 451
                                           ************************************************************************* PP

                             TIGR00133 435 kenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           + np++ve+ k+ k ++ +++vGqvmk t g+a+p+    ++k +l
  NCBI__GCF_003010935.1:WP_106716492.1 452 AANPDKVEQAKA-KPSLAGWFVGQVMKSTGGKANPQVLSDMVKSKL 496
                                           *******99765.78899***********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (500 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: 16.06
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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