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.27374.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: 10.01
//
[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:

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:

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:

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:

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