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.17430.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: 7.97
//
[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