Alignments for a candidate for gatB in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Pseudomonas fluorescens FW300-N1B4

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Pf1N1B4_1102 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102
          Length = 481

 Score =  457 bits (1175), Expect = e-133
 Identities = 227/480 (47%), Positives = 329/480 (68%), Gaps = 7/480 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M +E VIGLE+H +L T SK+FS S   FG+EPN+  +++DL  PGVLPV+N+ AV  A+
Sbjct: 1   MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
              +A++ EI   + F RKNYFYPD PK YQISQ + PI   G++DI + DG  KR+GIT
Sbjct: 61  MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTVKRVGIT 120

Query: 120 RLHMEEDAGKSTHK--GEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYT 177
           R H+EEDAGKS H+     + +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y 
Sbjct: 121 RAHLEEDAGKSLHEEFNGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYL 180

Query: 178 GVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLS 237
           G+ D  M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K +  E +RQ E +  
Sbjct: 181 GICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINTEVQRQIELIED 240

Query: 238 GGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPD 297
           GG++ Q+TR +D +  +T  MR KE ++DYRYFP+PD++P+ I+D++ + VR T+PELP 
Sbjct: 241 GGKVIQQTRLYDPNKDETRPMRSKEEANDYRYFPDPDLLPVVIEDSFLDDVRATLPELPP 300

Query: 298 ERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQV 357
           +++ ++  + GL  YDA VL  ++E +D+FE     G D KL +NW+M  +   LNK  +
Sbjct: 301 QKRERFQEQFGLSVYDASVLATSREQADYFEKVASIGGDAKLAANWVMVELGSLLNKQGL 360

Query: 358 ELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEAT 417
           ++  + ++ E L GM+  I+D T+S KIAK VF  +A   G+A +I++  GL Q++D   
Sbjct: 361 DIDQSPVSAEQLGGMLLRIKDNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTGA 420

Query: 418 LLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473
           +   ++E L  N + VE Y+      +GK  GF VGQ MKASKG+ANPQ VN+LLK +L+
Sbjct: 421 ISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKLE 480


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: 635
Number of extensions: 17
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: 475
Length of database: 481
Length adjustment: 34
Effective length of query: 441
Effective length of database: 447
Effective search space:   197127
Effective search space used:   197127
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 Pf1N1B4_1102 (Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7))
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.17940.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.5e-174  565.7   0.0   3.9e-174  565.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102  Aspartyl-tRNA(Asn) amidotransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102  Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.6   0.0  3.9e-174  3.9e-174       2     480 ..       1     479 [.       1     480 [. 0.98

  Alignments for each domain:
  == domain 1  score: 565.6 bits;  conditional E-value: 3.9e-174
                                      TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlkla 65 
                                                    +++e+viGlE+H+ql t+sK+F+ +s+ + + +pNt+ + v+lg+PG+lPvlN+eav++A++ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102   1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGS-EPNTQASLVDLGMPGVLPVLNQEAVRMAVMFG 63 
                                                    5789***************************.******************************** PP

                                      TIGR00133  66 lalnskivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEe 128
                                                    la++++i  +  vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i le++  k++gi+r hlEe
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102  64 LAIDAEIG-QHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTvKRVGITRAHLEE 126
                                                    ******55.79***********************************999888************ PP

                                      TIGR00133 129 DtgksqykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdle 192
                                                    D+gks ++e +    + +D+NR+g+PLlEiV++Pd++sakea+a++k +++++ryl+i dg++ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 127 DAGKSLHEEFN--GATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRYLGICDGNMA 188
                                                    ********775..7999*********************************************** PP

                                      TIGR00133 193 eGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafd 256
                                                    eGs+R+D+Nvsir+kGq ++gtr EiKN+ns++ iekai+ E++Rq++l+++g +v q+tr +d
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 189 EGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINTEVQRQIELIEDGGKVIQQTRLYD 252
                                                    **************************************************************** PP

                                      TIGR00133 257 ekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglsee 320
                                                     +k  t  +R+Kee++DYRYfp+Pdl p++i+++++++ v+++lpelP +kr+r+++++gls +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 253 PNKDETRPMRSKEEANDYRYFPDPDLLPVVIEDSFLDD-VRATLPELPPQKRERFQEQFGLSVY 315
                                                    ***********************************999.************************* PP

                                      TIGR00133 321 dakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaelikli 384
                                                    da vl + +e +d+fe+v++  +++kla+nW++ el + Lnk+ +++ ++ +++e+l  ++  i
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 316 DASVLATSREQADYFEKVASIGGDAKLAANWVMVELGSLLNKQGLDIDQSPVSAEQLGGMLLRI 379
                                                    **************************************************************** PP

                                      TIGR00133 385 kegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyk... 445
                                                    k+++is+k+ak ++e + + +++++++i+k+gl q++d+ ++ ++++e+++ n+++ve+y+   
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 380 KDNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTGAISAVLDEMLAANAEQVEQYRaad 443
                                                    ************************************************************9888 PP

                                      TIGR00133 446 .sgkekalkflvGqvmkktkgradpkevekllkell 480
                                                     +++ k+++f+vGq+mk +kg+a+p++v++llk +l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1102 444 eAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479
                                                    778899***************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.00
//
[ok]

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