Alignments for a candidate for fahA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Paraburkholderia bryophila 376MFSha3.1

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate H281DRAFT_04742 H281DRAFT_04742 fumarylacetoacetate hydrolase

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__Burk376:H281DRAFT_04742
          Length = 433

 Score =  504 bits (1299), Expect = e-147
 Identities = 239/408 (58%), Positives = 302/408 (74%), Gaps = 5/408 (1%)

Query: 10  SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKH--LFTGPVLSKHQDVFNQPTL 67
           +DF I NLP+G+FS   D  PR+GVAIGD+I+DL+ ++   L T P    +  VF + TL
Sbjct: 27  NDFSIQNLPFGIFSDSKDDTPRVGVAIGDEIVDLAALEAAGLLTVP---SNAGVFARDTL 83

Query: 68  NSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGDYTDF 127
           N F+ LG+ AW+  R+ L NLLS   A LRDD  LR  A + QA A +HLP  I  YTDF
Sbjct: 84  NEFIALGRDAWRSVRIQLSNLLSRDTATLRDDAALRAKALVRQADARLHLPVQIPGYTDF 143

Query: 128 YSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPDDSKP 187
           YSS++HATNVG MFR+ ++AL+PNW  +P+GY+GRASSVVVSGTP+RRP GQ+K  D + 
Sbjct: 144 YSSKEHATNVGSMFRNPKDALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQER 203

Query: 188 PVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWEYVPL 247
           PV+GAC+ LD+ELE  F +G GN LGEPI  + A  HIFGMVL+NDWSARDIQ+WEYVPL
Sbjct: 204 PVFGACRKLDIELETGFVIGGGNALGEPIACTDAEAHIFGMVLLNDWSARDIQQWEYVPL 263

Query: 248 GPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINLSVNLKGEG 307
           GPF  KSF TT+SPW+V +DAL PF V  P Q+P+PL YL HD  + FDI L V L+ +G
Sbjct: 264 GPFNSKSFTTTISPWIVTLDALEPFRVAQPVQEPQPLAYLRHDGEHAFDIALEVTLRPQG 323

Query: 308 MSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENFGSMLELSW 367
             QA TI ++NFKYMYWTM QQL HH+V GCN R GDL+ SGTISGP  +++GS+LEL+ 
Sbjct: 324 AKQATTIARTNFKYMYWTMAQQLAHHTVGGCNTRVGDLMGSGTISGPTEDSYGSLLELTL 383

Query: 368 KGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415
            G KP++L  G TR F+ DGDE+ ++G+CQ DGYR+GFG C G++LPA
Sbjct: 384 NGKKPLELNEGGTRSFIEDGDELTLSGWCQADGYRVGFGTCVGEILPA 431


Lambda     K      H
   0.321    0.139    0.440 

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: 593
Number of extensions: 18
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: 433
Length adjustment: 32
Effective length of query: 387
Effective length of database: 401
Effective search space:   155187
Effective search space used:   155187
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 H281DRAFT_04742 H281DRAFT_04742 (fumarylacetoacetate hydrolase)
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.32101.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.2e-190  617.6   0.0   5.9e-190  617.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04742  H281DRAFT_04742 fumarylacetoacet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04742  H281DRAFT_04742 fumarylacetoacetate hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.4   0.0  5.9e-190  5.9e-190       1     419 [.      17     431 ..      17     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 617.4 bits;  conditional E-value: 5.9e-190
                                    TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfk 64 
                                                  s+v++a+    df++qnlP+G+fs ++d ++r+gvaiGd+i+dl+++ aagl++     +++ vf 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742  17 SWVQSANepSNDFSIQNLPFGIFSDSKDDTPRVGVAIGDEIVDLAALEAAGLLTV---PSNAGVFA 79 
                                                  8*****96668****************************************9987...67899*** PP

                                    TIGR01266  65 estlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfys 130
                                                  + tln f+algr a++ vr +l +lls ++++lrd+aalr +al+ qa+a+ hlP+qi  ytdfys
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742  80 RDTLNEFIALGRDAWRSVRIQLSNLLSRDTATLRDDAALRAKALVRQADARLHLPVQIPGYTDFYS 145
                                                  ****************************************************************** PP

                                    TIGR01266 131 sirhatnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckk 196
                                                  s +hatnvG +fr +++allPn+  +P+gy GrassvvvsGt++rrP+Gq+k ++ + Pvfg+c+k
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742 146 SKEHATNVGSMFRNPKDALLPNWSEMPIGYNGRASSVVVSGTPVRRPNGQLKLPDQERPVFGACRK 211
                                                  ****************************************************************** PP

                                    TIGR01266 197 ldlelelaffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsP 262
                                                  ld+ele +f +g +n+lGe++    ae hifG+vllndwsardiq+weyvPlGPf++ksf+tt+sP
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742 212 LDIELETGFVIGGGNALGEPIACTDAEAHIFGMVLLNDWSARDIQQWEYVPLGPFNSKSFTTTISP 277
                                                  ****************************************************************** PP

                                    TIGR01266 263 wvvsiealePfrvaqlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslyw 328
                                                  w+v+++alePfrva  +P+q+p+pl+ylr+d  + afdi lev+l+++G ++a++i+r+n+k +yw
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742 278 WIVTLDALEPFRVA--QPVQEPQPLAYLRHD-GEHAFDIALEVTLRPQGAKQATTIARTNFKYMYW 340
                                                  *************9..9**************.999******************************* PP

                                    TIGR01266 329 tlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdev 394
                                                  t++qqlahh+v Gcn r Gdl+gsGtisG+ e+++Gsllel+ +Gkk+++l +g tr f+edGde+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742 341 TMAQQLAHHTVGGCNTRVGDLMGSGTISGPTEDSYGSLLELTLNGKKPLELNEGGTRSFIEDGDEL 406
                                                  ****************************************************************** PP

                                    TIGR01266 395 ilrgvckkeGvrvGfGecaGkvlpa 419
                                                   l+g c+ +G+rvGfG c G++lpa
  lcl|FitnessBrowser__Burk376:H281DRAFT_04742 407 TLSGWCQADGYRVGFGTCVGEILPA 431
                                                  ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (433 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: 11.56
//
[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