Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Cupriavidus basilensis 4G11

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate RR42_RS09905 RR42_RS09905 fumarylacetoacetase

Query= SwissProt::P25093
         (419 letters)



>FitnessBrowser__Cup4G11:RR42_RS09905
          Length = 437

 Score =  338 bits (868), Expect = 1e-97
 Identities = 191/427 (44%), Positives = 254/427 (59%), Gaps = 25/427 (5%)

Query: 7   AEDSDFPIQNLPYGVFSTQSNPKP-RIGVAIGDQILDLSVIKHLFTGPVL----SKHQHV 61
           A   DFP+QNLP  VF  + + +  R GVAIGDQI+DL  ++ L   P L    ++    
Sbjct: 20  AAGCDFPLQNLPLSVFRRKGSTEAWRGGVAIGDQIVDLGALQSL---PGLQDSAAEAVRA 76

Query: 62  FDETTLNSFMGLGQAAWKEARASLQNLLSASQAQLRDDKELRQRAFTSQASATMHLPATI 121
               TLN  + LG  +W+  R  L  LL +  +  R  +E    A   Q  A   +P  I
Sbjct: 77  AAAPTLNGLLELGPESWRALRHGLYGLLQSGSSLARQVRE----ALVPQLDAEHAVPVRI 132

Query: 122 GDYTDFYSSLQHATNVGIMFRGKENALLPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMR 181
           GDYTDFY+SL HA N    F  + N   PN+  LP+ YHGR SS+ VSG  + RP GQ R
Sbjct: 133 GDYTDFYTSLDHAVNCCRQFGIEVN---PNFDWLPIAYHGRVSSIDVSGQQVYRPAGQYR 189

Query: 182 PDNSKPPVYGASKRLDMELEMAFFVGPGNRFGEPIPISKAQEHIFGMVLMNDWSARDIQQ 241
            D S  PVYG  +RLD ELE+   +G GN  G PIP++ AQ+HIFG+ L+NDWSARDIQ 
Sbjct: 190 TDPSSAPVYGPCQRLDYELEVGAVIGIGNARGTPIPLANAQQHIFGLCLLNDWSARDIQT 249

Query: 242 WEYVPLGPFLGKSFGTTISPWVVPMDALMPFVV--PNPKQDPKPLPYL---CHSQPYTFD 296
           WE  PLGPFL K+F TT+SPW+V ++AL+P+        + P+PL YL    ++    FD
Sbjct: 250 WEMQPLGPFLAKNFATTLSPWIVTLEALLPYRTGWTRAPERPQPLDYLRSADNAAAGAFD 309

Query: 297 INLSVA-LKGEGMSQAA---TICRSNFKHMYWTILQQLTHHSVNGCNLRPGDLLASGTIS 352
           I L V+ L     +Q      + R++F+H YWT+ Q + HH+V GCNL+PGDLL SGT+S
Sbjct: 310 IQLEVSILSARRQAQGRPPHKLTRTSFQHQYWTLGQMIAHHTVGGCNLQPGDLLGSGTVS 369

Query: 353 GSDPESFGSMLELSWKGTKAIDVGQGQTRTFLLDGDEVIITGHCQGDGY-RVGFGQCAGK 411
           G +P   G+++EL+  GT   D+G G+ R FL DGD V+  G C+ + Y R+GFG     
Sbjct: 370 GPNPWEAGALIELTVSGTHPADIGDGEQRGFLKDGDTVVFRGWCEREDYARIGFGVNYAT 429

Query: 412 VLPALSP 418
           VLPA  P
Sbjct: 430 VLPAPGP 436


Lambda     K      H
   0.320    0.136    0.422 

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: 582
Number of extensions: 29
Number of successful extensions: 7
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: 437
Length adjustment: 32
Effective length of query: 387
Effective length of database: 405
Effective search space:   156735
Effective search space used:   156735
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 RR42_RS09905 RR42_RS09905 (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.1159.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-143  464.5   0.0   1.8e-143  464.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS09905  RR42_RS09905 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS09905  RR42_RS09905 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.3   0.0  1.8e-143  1.8e-143       1     419 [.      13     433 ..      13     434 .. 0.93

  Alignments for each domain:
  == domain 1  score: 464.3 bits;  conditional E-value: 1.8e-143
                                 TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkads.srrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 
                                               s++++a+   +dfplqnlP+ vf  k ++   r gvaiGdqi+dl ++++  ++++ ++ e+  +    
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905  13 SWLDSANaaGCDFPLQNLPLSVFRRKGSTeAWRGGVAIGDQIVDLGALQSLPGLQD-SAAEAVRAAAAP 80 
                                               79988885467************976544156899***************888887.567788889999 PP

                                 TIGR01266  67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135
                                               tln +l lg  +++++r+ l  ll + +      a++ +eal++q +a+  +P++iGdytdfy+s+ ha
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905  81 TLNGLLELGPESWRALRHGLYGLLQSGSSL----ARQVREALVPQLDAEHAVPVRIGDYTDFYTSLDHA 145
                                               ************************976666....777889***************************** PP

                                 TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204
                                                n    f      + Pn+ +lP++yhGr ss+ vsG ++ rP Gq ++d ++ Pv+gpc++ld+ele++
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905 146 VNCCRQFG---IEVNPNFDWLPIAYHGRVSSIDVSGQQVYRPAGQYRTDPSSAPVYGPCQRLDYELEVG 211
                                               ****9998...5678****************************************************** PP

                                 TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273
                                                 +g +n+ G+++p+ +a++hifG++llndwsardiq+we +PlGPflak+fatt+sPw+v++eal P+
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905 212 AVIGIGNARGTPIPLANAQQHIFGLCLLNDWSARDIQTWEMQPLGPFLAKNFATTLSPWIVTLEALLPY 280
                                               ********************************************************************* PP

                                 TIGR01266 274 rvaqlePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlah 336
                                               r+  ++  ++p+pl ylr  +  a  afdi+levs+ ++  +     +++++r+ +++ ywtl q++ah
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905 281 RTGWTRAPERPQPLDYLRSADnaAAGAFDIQLEVSILSARRQAqgrpPHKLTRTSFQHQYWTLGQMIAH 349
                                               ***99*9**********975435889**********987654456779********************* PP

                                 TIGR01266 337 hsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGv 405
                                               h+v Gcnl++GdllgsGt+sG+++ + G+l+el+  G+++ +++dge+r fl+dGd+v++rg c++e +
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905 350 HTVGGCNLQPGDLLGSGTVSGPNPWEAGALIELTVSGTHPADIGDGEQRGFLKDGDTVVFRGWCEREDY 418
                                               ******************************************************************998 PP

                                 TIGR01266 406 r.vGfGecaGkvlpa 419
                                                 +GfG    +vlpa
  lcl|FitnessBrowser__Cup4G11:RR42_RS09905 419 ArIGFGVNYATVLPA 433
                                               77***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (437 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: 00:00:00.02
# Mc/sec: 7.88
//
[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