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_RS11790 BPHYT_RS11790 fumarylacetoacetase

Query= BRENDA::Q8RW90
         (421 letters)



>FitnessBrowser__BFirm:BPHYT_RS11790
          Length = 440

 Score =  335 bits (859), Expect = 2e-96
 Identities = 185/416 (44%), Positives = 253/416 (60%), Gaps = 16/416 (3%)

Query: 16  FPIQNLPYGVFKPE-SNSTPRPAVAIGDLVLDLSAISEAGLFDGLILKDADCFLQPNLNK 74
           FPIQNLP+ VF+   S+   R AVAIGD V+D++A +     +G+  + A    QP LN+
Sbjct: 27  FPIQNLPFSVFRRRHSDEAFRGAVAIGDQVIDIAAWASRAGLNGIAGEGARVCAQPVLNE 86

Query: 75  FLAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKVEMIVPMVIGDYTDFFA 134
           F +MG  AW+  R  L   L    P   D+           S+VE  +P  IGDYTDF+ 
Sbjct: 87  FFSMGPSAWRAVRHALFAALHERAP--SDDRAALEACLIPQSEVEYGLPAQIGDYTDFYT 144

Query: 135 SMHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDIIRPRGQGHPQGNSEPY 194
           S+HHA N   +     + +  N+  +PIAYHGR SSI +SG    RP GQ    G   P 
Sbjct: 145 SIHHATNISKLLG--LSGVGANFKSIPIAYHGRVSSIGLSGQRFRRPAGQIMLPGEDAPI 202

Query: 195 FGPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMNDWSARDIQAWEYVPLGP 254
           F PS+KLD+ELE+   +G GN  G+PI ++ A  H+FGL L+NDWSARDIQAWE  PLGP
Sbjct: 203 FSPSRKLDYELELGIYIGQGNAAGEPIALDQADSHVFGLCLLNDWSARDIQAWEMQPLGP 262

Query: 255 FLGKSFGTTISPWIVTLDALEPFGCQAPK--QDPPPLPYL-AEKESVN--YDISLEVQLK 309
           FL K+F TTISPWIVT++AL PF    P+   D  PLPYL +++ S     DI LEV ++
Sbjct: 263 FLAKNFATTISPWIVTMEALAPFRLPLPRPHTDGKPLPYLDSDRNSTTGAIDIQLEVCIE 322

Query: 310 PS----GRDDSCVITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISGPEPDSYG 365
            S    G   +  ++ ++F++ YW+I Q +AHH   GCNLR GDLLG+GTISGP     G
Sbjct: 323 TSRHQAGNLPAAQLSLTSFRHQYWSIAQMVAHHAAGGCNLRAGDLLGSGTISGPGQSEAG 382

Query: 366 CLLELTWNGQKPLSLN-GTTQTFLEDGDQVTFSGVCKGDGY-NVGFGTCTGKIVPS 419
            L+EL  N  +P++LN G  ++++EDGD +   G C+  G+  +GFG   G+++P+
Sbjct: 383 ALMELARNASEPVTLNTGEKRSYVEDGDAIILRGYCEKAGFARIGFGESRGEVLPA 438


Lambda     K      H
   0.319    0.139    0.434 

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: 560
Number of extensions: 18
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: 421
Length of database: 440
Length adjustment: 32
Effective length of query: 389
Effective length of database: 408
Effective search space:   158712
Effective search space used:   158712
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate BPHYT_RS11790 BPHYT_RS11790 (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.16198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     5e-149  482.6   0.0   5.7e-149  482.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS11790  BPHYT_RS11790 fumarylacetoacetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS11790  BPHYT_RS11790 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.4   0.0  5.7e-149  5.7e-149       1     419 [.      15     438 ..      15     439 .. 0.95

  Alignments for each domain:
  == domain 1  score: 482.4 bits;  conditional E-value: 5.7e-149
                                TIGR01266   1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfeglalkehqevfkest 67 
                                              s+v++a+   +dfp+qnlP+ vf  + +d   r +vaiGdq++d+++ a+ ++++g  ++e + v  +  
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790  15 SWVESANapTCDFPIQNLPFSVFRRRhSDEAFRGAVAIGDQVIDIAAWASRAGLNG-IAGEGARVCAQPV 83 
                                              89999997789************976245667899***************9*****.88999******** PP

                                TIGR01266  68 lnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatn 137
                                              ln f+++g +a+++vr+ l   l e a    d++a  +  l++q+e++  lPaqiGdytdfy+si+hatn
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790  84 LNEFFSMGPSAWRAVRHALFAALHERAPS--DDRAALEACLIPQSEVEYGLPAQIGDYTDFYTSIHHATN 151
                                              *********************99966665..88888899******************************* PP

                                TIGR01266 138 vGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffv 207
                                              + +l+      +  n+k +P++yhGr ss+  sG   rrP Gqi  ++ + P+f+p++kld+elel++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790 152 ISKLLG--LSGVGANFKSIPIAYHGRVSSIGLSGQRFRRPAGQIMLPGEDAPIFSPSRKLDYELELGIYI 219
                                              ****98..577899******************************************************** PP

                                TIGR01266 208 gtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaq 277
                                              g++n+ Ge++ +++a+ h+fG++llndwsardiqawe +PlGPflak+fatt+sPw+v++eal Pfr + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790 220 GQGNAAGEPIALDQADSHVFGLCLLNDWSARDIQAWEMQPLGPFLAKNFATTISPWIVTMEALAPFRLPL 289
                                              ********************************************************************** PP

                                TIGR01266 278 lePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlahhsvnG 341
                                               +P+ d kplpyl  dr     a+di+lev ++t   +     aa++s + +++ yw+++q++ahh+  G
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790 290 PRPHTDGKPLPYLDSDRnsTTGAIDIQLEVCIETSRHQAgnlpAAQLSLTSFRHQYWSIAQMVAHHAAGG 359
                                              **************9995456689******998765444445599************************* PP

                                TIGR01266 342 cnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvr.vGfG 410
                                              cnlraGdllgsGtisG+ + + G+l+el+ + +++v l  ge+r ++edGd +ilrg c+k G   +GfG
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790 360 CNLRAGDLLGSGTISGPGQSEAGALMELARNASEPVTLNTGEKRSYVEDGDAIILRGYCEKAGFArIGFG 429
                                              ***************************************************************877**** PP

                                TIGR01266 411 ecaGkvlpa 419
                                              e +G+vlpa
  lcl|FitnessBrowser__BFirm:BPHYT_RS11790 430 ESRGEVLPA 438
                                              ********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (440 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: 11.64
//
[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