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_RS31270 RR42_RS31270 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__Cup4G11:RR42_RS31270
          Length = 420

 Score =  489 bits (1259), Expect = e-143
 Identities = 239/417 (57%), Positives = 303/417 (72%), Gaps = 5/417 (1%)

Query: 2   SFIPVAED--SDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQ 59
           S+I  A D  + FP+ NLPYG+FS  G   PR+GVAIGD ILDLS++      P   K  
Sbjct: 7   SWIESANDGVTHFPLQNLPYGIFSPNGQG-PRVGVAIGDFILDLSVLDEAGLLPACVK-- 63

Query: 60  DVFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPA 119
            VF   TLN+F+ LG+ AW E R  L ++L+     L   + L + A +  A AT+HLP 
Sbjct: 64  GVFGGATLNAFIALGKPAWTETRQRLTSMLAADDTTLHPKSALHEQALVPMAWATLHLPV 123

Query: 120 TIGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQ 179
            I  YTDFYSSR+HATNVG MFRD +NAL+PNWL +P+GY+GRASSVVVSGT +RRP GQ
Sbjct: 124 DIPGYTDFYSSREHATNVGRMFRDPDNALLPNWLEIPIGYNGRASSVVVSGTELRRPKGQ 183

Query: 180 MKPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDI 239
           +KP ++  PV+ AC+ LD ELEMAF VG  + LGEP+  + A  H+FGMV++NDWSARDI
Sbjct: 184 IKPPNAPRPVFTACQKLDYELEMAFIVGKPSTLGEPVSTAAAAGHMFGMVILNDWSARDI 243

Query: 240 QKWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINL 299
           Q+WEYVPLGPF  K FGT++SPWVV MDAL PF   NP Q P PL YL   E   +DI L
Sbjct: 244 QQWEYVPLGPFNSKGFGTSISPWVVTMDALEPFRRDNPVQSPEPLAYLQQPERNAYDIAL 303

Query: 300 SVNLKGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENF 359
            V+L+ EG +QA T+C++NFK MYWTM+QQL HH+V+GCN+R GDL+ SGTISG  P+++
Sbjct: 304 EVSLRPEGAAQATTVCRTNFKAMYWTMVQQLAHHTVSGCNVRVGDLMGSGTISGTTPDSY 363

Query: 360 GSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPAL 416
           GS+LEL+  G +P+ L +G  R FL DGDEV++ G+CQGDGYR+GFG+ AGK+LPAL
Sbjct: 364 GSLLELTRNGAEPLTLADGSKRGFLEDGDEVVMAGWCQGDGYRVGFGEVAGKILPAL 420


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: 647
Number of extensions: 24
Number of successful extensions: 3
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: 420
Length adjustment: 32
Effective length of query: 387
Effective length of database: 388
Effective search space:   150156
Effective search space used:   150156
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: 50 (23.9 bits)

Align candidate RR42_RS31270 RR42_RS31270 (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.26593.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-186  604.4   0.0     6e-186  604.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS31270  RR42_RS31270 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS31270  RR42_RS31270 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  604.3   0.0    6e-186    6e-186       1     420 []       7     420 .]       7     420 .] 0.98

  Alignments for each domain:
  == domain 1  score: 604.3 bits;  conditional E-value: 6e-186
                                 TIGR01266   1 sfvavakn..sdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkest 67 
                                               s++++a++  + fplqnlPyG+fs  +++ +r+gvaiGd ildls++ +agl+        + vf ++t
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270   7 SWIESANDgvTHFPLQNLPYGIFS-PNGQGPRVGVAIGDFILDLSVLDEAGLLPA----CVKGVFGGAT 70 
                                               899999963379************.78899*********************9988....4578****** PP

                                 TIGR01266  68 lnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhat 136
                                               lnaf+alg+pa++e r+rl  +l+++  +l  ++al+++al+++a at hlP+ i  ytdfyss++hat
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270  71 LNAFIALGKPAWTETRQRLTSMLAADDTTLHPKSALHEQALVPMAWATLHLPVDIPGYTDFYSSREHAT 139
                                               ********************************************************************* PP

                                 TIGR01266 137 nvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaf 205
                                               nvG +fr +dnallPn+  +P+gy GrassvvvsGtelrrP+Gqik++na  Pvf++c+kld+ele+af
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 140 NVGRMFRDPDNALLPNWLEIPIGYNGRASSVVVSGTELRRPKGQIKPPNAPRPVFTACQKLDYELEMAF 208
                                               ********************************************************************* PP

                                 TIGR01266 206 fvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfr 274
                                                vg++ +lGe+v    a+ h+fG+v+lndwsardiq+weyvPlGPf++k f+t++sPwvv+++alePfr
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 209 IVGKPSTLGEPVSTAAAAGHMFGMVILNDWSARDIQQWEYVPLGPFNSKGFGTSISPWVVTMDALEPFR 277
                                               ********************************************************************* PP

                                 TIGR01266 275 vaqlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcn 343
                                               +   +P+q p+pl+yl++  +  a+di levsl++eG a+a++++r+n+k +ywt+ qqlahh+v+Gcn
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 278 RD--NPVQSPEPLAYLQQP-ERNAYDIALEVSLRPEGAAQATTVCRTNFKAMYWTMVQQLAHHTVSGCN 343
                                               **..*************99.999********************************************** PP

                                 TIGR01266 344 lraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGec 412
                                               +r Gdl+gsGtisG+ ++++Gsllel+ +G++++ ladg++r fledGdev++ g c+ +G+rvGfGe 
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 344 VRVGDLMGSGTISGTTPDSYGSLLELTRNGAEPLTLADGSKRGFLEDGDEVVMAGWCQGDGYRVGFGEV 412
                                               ********************************************************************* PP

                                 TIGR01266 413 aGkvlpal 420
                                               aGk+lpal
  lcl|FitnessBrowser__Cup4G11:RR42_RS31270 413 AGKILPAL 420
                                               ******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (420 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: 11.89
//
[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