Alignments for a candidate for hutG in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG in Burkholderia phytofirmans PsJN

Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate BPHYT_RS21925 BPHYT_RS21925 formimidoylglutamase

Query= reanno::Koxy:BWI76_RS08725
         (318 letters)



>FitnessBrowser__BFirm:BPHYT_RS21925
          Length = 320

 Score =  216 bits (551), Expect = 4e-61
 Identities = 132/319 (41%), Positives = 177/319 (55%), Gaps = 14/319 (4%)

Query: 6   PTPAALWQGRDDSAEAANALRLFQTIVRAERFEPEMLA-GDIALL-GFACDEGVRRNKGR 63
           P    +W GR D  E  +  R+F  IV    F+  + A GD  ++ GF  DEGVRRN+GR
Sbjct: 4   PFDDKMWAGRSDDGEPGDTRRVFNQIVP---FDGSLRAHGDTTVVVGFGSDEGVRRNQGR 60

Query: 64  TGAERGPETLRRALANMASHDGHDRCVDMGTIHVADDALEAAQQALREAVTACQRAGKRT 123
           TGA   P+ LRRALA + + +      D G +   D  LE AQ  L   ++    +G R 
Sbjct: 61  TGAAHAPKELRRALAGLPAKNSMAMLADAGDVACDDGDLEGAQAELANVISEVLASGGRP 120

Query: 124 LVLGGGHETAFGHGAGVL---------DAFPGEEVGIINLDAHLDLRIADRASSGTPFRQ 174
           LV GGGHE A+    G++         ++    ++ IIN DAH DLR    A+SGTPF Q
Sbjct: 121 LVFGGGHEVAWATYCGLVLHQHRREADESATPRKLLIINFDAHFDLRQKRPANSGTPFDQ 180

Query: 175 LALACEAQRRAFHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELARN 234
           +A  C  +R  F+Y C G+S   NT +L   A R GV    D+D+        + EL   
Sbjct: 181 IANDCAERRVPFNYVCFGISDLGNTASLFVHAQRLGVRYALDVDMQETQLPLRLQELDLM 240

Query: 235 IARYDRLYLTIDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEFNP 294
           +   D +YLTIDLDVLPA   P VSAPAALG+PL  +  +V  +  SGKL+A D+ E+NP
Sbjct: 241 LDEADDVYLTIDLDVLPAATAPGVSAPAALGVPLFVVEEMVRRVRGSGKLRAADIAEYNP 300

Query: 295 QYDIDSQGARAAARLAWQI 313
             D D + ARAAARLA+++
Sbjct: 301 SLDQDRRTARAAARLAYRL 319


Lambda     K      H
   0.322    0.135    0.408 

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: 296
Number of extensions: 19
Number of successful extensions: 3
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: 318
Length of database: 320
Length adjustment: 28
Effective length of query: 290
Effective length of database: 292
Effective search space:    84680
Effective search space used:    84680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS21925 BPHYT_RS21925 (formimidoylglutamase)
to HMM TIGR01227 (hutG: formimidoylglutamase (EC 3.5.3.8))

# 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.carbon/TIGR01227.hmm
# target sequence database:        /tmp/gapView.19618.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01227  [M=307]
Accession:   TIGR01227
Description: hutG: formimidoylglutamase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.3e-92  296.2   0.0    1.5e-92  296.1   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS21925  BPHYT_RS21925 formimidoylglutama


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS21925  BPHYT_RS21925 formimidoylglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.1   0.0   1.5e-92   1.5e-92       1     304 [.      10     318 ..      10     320 .] 0.93

  Alignments for each domain:
  == domain 1  score: 296.1 bits;  conditional E-value: 1.5e-92
                                TIGR01227   1 lqgrldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairqalan 70 
                                              + gr d  e ++ rr+++ + + d + l   ++   ++++G+ +d+gv+rn+GrtGA +aP+ +r+ala+
  lcl|FitnessBrowser__BFirm:BPHYT_RS21925  10 WAGRSDDGEPGDTRRVFNQIVPFDGS-L--RAHGDTTVVVGFGSDEGVRRNQGRTGAAHAPKELRRALAG 76 
                                              77888888888999998888888874.3..456667899******************************* PP

                                TIGR01227  71 lgdlvasealyDlGdivlegddlvdaqkevaqavaelladarvvvllGGdneiayatikalaqa....ak 136
                                              l++ + + +l+D+Gd+ ++++dl+ aq+e+a+++ e+la++ ++++ GG++e+a+at+ +l+ +      
  lcl|FitnessBrowser__BFirm:BPHYT_RS21925  77 LPAKNSMAMLADAGDVACDDGDLEGAQAELANVISEVLASGGRPLVFGGGHEVAWATYCGLVLHqhrrE- 145
                                              ************************************************************987743331. PP

                                TIGR01227 137 gek.......riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivlGirrfsntqalfdy 197
                                                        +  +infDAHfDlR+     + sGTpf q+++ + +    f++++ Gi+ ++nt++lf +
  lcl|FitnessBrowser__BFirm:BPHYT_RS21925 146 --AdesatprKLLIINFDAHFDLRQKR--PANSGTPFDQIANDCAERRvpFNYVCFGISDLGNTASLFVH 211
                                              ..13446777788***********998..999************999999******************** PP

                                TIGR01227 198 akkkgvryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPGvsApaagGleleellelv 267
                                              a+++gvry +d  ++e++l+  ++ l+ +lde D +ylt+dlDVl+aa APGvsApaa G+ l +++e+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS21925 212 AQRLGVRYALDVDMQETQLPLRLQELDLMLDEADDVYLTIDLDVLPAATAPGVSAPAALGVPLFVVEEMV 281
                                              ********************************************************************** PP

                                TIGR01227 268 kriaasdkvrgveivEvnPtlDaddrTarlaArlvah 304
                                              +r+  s+k+r ++i+E+nP+lD d rTar+aArl   
  lcl|FitnessBrowser__BFirm:BPHYT_RS21925 282 RRVRGSGKLRAADIAEYNPSLDQDRRTARAAARLAYR 318
                                              *********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (320 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: 7.22
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources