Alignments for a candidate for fahA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Burkholderia phytofirmans PsJN

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate BPHYT_RS03805 BPHYT_RS03805 fumarylacetoacetase

Query= BRENDA::P35505
         (419 letters)



>FitnessBrowser__BFirm:BPHYT_RS03805
          Length = 436

 Score =  499 bits (1285), Expect = e-146
 Identities = 241/419 (57%), Positives = 302/419 (72%), Gaps = 4/419 (0%)

Query: 2   SFIPVAEDS--DFPIQNLPYGVFSTQSNPKPRIGVAIGDQILDLSVIKH--LFTGPALSK 57
           S++  A DS  DF IQNLP+GVFS   N   R+GVAIGD I+DL+ ++   L + P+ + 
Sbjct: 17  SWVESANDSTNDFSIQNLPFGVFSDHLNATRRVGVAIGDGIVDLAALESAGLLSVPSSAA 76

Query: 58  HQHVFDETTLNNFMGLGQAAWKEARASLQNLLSASQARLRDDKELRQRAFTSQASATMHL 117
              VF    LN+F+ LG+ AW+  R  L  LLS   A LRDD ELR RA   QA A +HL
Sbjct: 77  GNSVFVRDALNDFIALGRDAWRGVRIQLSKLLSRDNATLRDDAELRGRALIRQADAQLHL 136

Query: 118 PATIGDYTDFYSSRQHATNVGIMFRGKENALLPNWLHLPVGYHGRASSIVVSGTPIRRPM 177
           P  I  YTDFYSS++HATNVG MFR  +NALLPNW  +P+GY+GRASS+VVSGTP+RRP 
Sbjct: 137 PVQIPGYTDFYSSKEHATNVGSMFRDPKNALLPNWSEMPIGYNGRASSVVVSGTPVRRPN 196

Query: 178 GQMRPDNSKPPVYGACRLLDMELEMAFFVGPGNRFGEPIPISKAHEHIFGMVLMNDWSAR 237
           GQ++  +   PV+GACR LD+ELE  F +G GN  GEP+  + A  HIFGMVL+NDWSAR
Sbjct: 197 GQLKLPDQDRPVFGACRKLDIELETGFVIGAGNALGEPVACADAEAHIFGMVLLNDWSAR 256

Query: 238 DIQQWEYVPLGPFLGKSFGTTISPWVVPMDALMPFVVPNPKQDPKPLPYLCHSQPYTFDI 297
           DIQQWEYVPLGPF  K F TTISPW+V +DAL PF V  P Q+ +PL YL H   + FDI
Sbjct: 257 DIQQWEYVPLGPFNSKGFATTISPWIVTLDALEPFRVAQPAQELQPLAYLRHEGEHAFDI 316

Query: 298 NLSVSLKGEGMSQAATICRSNFKHMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGSDPE 357
            L V L+ +   +A+TI R+NFKHMYWTM QQL HH+V+GCN R GDL+ SGTISG   +
Sbjct: 317 TLEVRLRPQQAKEASTISRTNFKHMYWTMAQQLAHHTVSGCNTRVGDLMGSGTISGPTED 376

Query: 358 SFGSMLELSWKGTKAIDVEQGQTRTFLLDGDEVIITGHCQGDGYRVGFGQCAGKVLPAL 416
           SFGS+LE++W G K +++++G TR+F+ DGDE+ + G CQGDGYRVGFG C G++LPAL
Sbjct: 377 SFGSLLEMTWNGKKPLNLQEGGTRSFIEDGDELTLAGWCQGDGYRVGFGACVGEILPAL 435


Lambda     K      H
   0.320    0.136    0.426 

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: 605
Number of extensions: 21
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: 419
Length of database: 436
Length adjustment: 32
Effective length of query: 387
Effective length of database: 404
Effective search space:   156348
Effective search space used:   156348
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate BPHYT_RS03805 BPHYT_RS03805 (fumarylacetoacetase)
to HMM TIGR01266 (fahA: fumarylacetoacetase (EC 3.7.1.2))

# 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/TIGR01266.hmm
# target sequence database:        /tmp/gapView.1397.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01266  [M=420]
Accession:   TIGR01266
Description: fum_ac_acetase: fumarylacetoacetase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.2e-189  616.4   0.0   1.3e-189  616.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS03805  BPHYT_RS03805 fumarylacetoacetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS03805  BPHYT_RS03805 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.3   0.0  1.3e-189  1.3e-189       1     420 []      17     435 ..      17     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 616.3 bits;  conditional E-value: 1.3e-189
                                TIGR01266   1 sfvavakns..dfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestl 68 
                                              s+v++a++s  df++qnlP+Gvfs + +++rr+gvaiGd i+dl+++ +agl++ ++  + + vf + +l
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805  17 SWVESANDStnDFSIQNLPFGVFSDHLNATRRVGVAIGDGIVDLAALESAGLLSVPSSAAGNSVFVRDAL 86 
                                              8*****965559********************************************************** PP

                                TIGR01266  69 naflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnv 138
                                              n f+algr a++ vr +l klls ++++lrd+a+lr +al+ qa+a+ hlP+qi  ytdfyss +hatnv
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805  87 NDFIALGRDAWRGVRIQLSKLLSRDNATLRDDAELRGRALIRQADAQLHLPVQIPGYTDFYSSKEHATNV 156
                                              ********************************************************************** PP

                                TIGR01266 139 GilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvg 208
                                              G +fr ++nallPn+  +P+gy GrassvvvsGt++rrP+Gq+k ++ + Pvfg+c+kld+ele +f +g
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805 157 GSMFRDPKNALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQDRPVFGACRKLDIELETGFVIG 226
                                              ********************************************************************** PP

                                TIGR01266 209 tenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaql 278
                                               +n+lGe+v    ae hifG+vllndwsardiq+weyvPlGPf++k fatt+sPw+v+++alePfrva  
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805 227 AGNALGEPVACADAEAHIFGMVLLNDWSARDIQQWEYVPLGPFNSKGFATTISPWIVTLDALEPFRVA-- 294
                                              *******************************************************************9.. PP

                                TIGR01266 279 ePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGd 348
                                              +P q+ +pl+ylr++  + afdi lev l+++  +ea++isr+n+k++ywt++qqlahh+v+Gcn r Gd
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805 295 QPAQELQPLAYLRHE-GEHAFDITLEVRLRPQQAKEASTISRTNFKHMYWTMAQQLAHHTVSGCNTRVGD 363
                                              9**************.999*************************************************** PP

                                TIGR01266 349 llgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGecaGkvlp 418
                                              l+gsGtisG+ e++fGslle++++Gkk+++l +g tr f+edGde+ l g c+ +G+rvGfG c G++lp
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805 364 LMGSGTISGPTEDSFGSLLEMTWNGKKPLNLQEGGTRSFIEDGDELTLAGWCQGDGYRVGFGACVGEILP 433
                                              ********************************************************************** PP

                                TIGR01266 419 al 420
                                              al
  lcl|FitnessBrowser__BFirm:BPHYT_RS03805 434 AL 435
                                              95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (436 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.31
//
[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