Alignments for a candidate for fahA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Echinicola vietnamensis KMM 6221, DSM 17526

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate Echvi_2481 Echvi_2481 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>FitnessBrowser__Cola:Echvi_2481
          Length = 425

 Score =  447 bits (1150), Expect = e-130
 Identities = 228/420 (54%), Positives = 304/420 (72%), Gaps = 9/420 (2%)

Query: 1   MKSFVSVPQNSDFPIQNLPYGVFSTKADSSRHIGVAIGDQILNLAEIANLFDGPQLKAHQ 60
           +KS+V +P+NSDF I NLP+GVF  K  S R IG+AIGD+I++L  +        +   +
Sbjct: 9   LKSWVQIPKNSDFTIYNLPFGVFRNKRLSPR-IGMAIGDKIVDLHVLFCEGFFSSIHLPE 67

Query: 61  DVFKQSTLNAFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQSDATMHLPA 120
           +VF + +LN FMAL +P   + R  +Q+LL E+   L+D+   R + +V + +A M +P 
Sbjct: 68  EVFLKDSLNEFMALGKPMTRKVREMVQELLLEENTALKDH-RARGKVMVNRKEAKMLMPV 126

Query: 121 QIGDYTDFYSSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGTDLKRPVGQ 180
           ++GDYTDFYSS  HATNVG MFR  ENALMPNWK LPVGYHGRASSIV SGT + RP GQ
Sbjct: 127 KVGDYTDFYSSKEHATNVGTMFRDPENALMPNWKHLPVGYHGRASSIVPSGTPIHRPKGQ 186

Query: 181 TKAPDAEVPSFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVLMNDWSARD 240
            KAPDAE PSFGPS+ +DFELEMAF    P  ++GT +  ++AE+ IFG VL NDWSARD
Sbjct: 187 FKAPDAEKPSFGPSRRLDFELEMAFITSNP-TKMGTSIRTQEAEEHIFGFVLFNDWSARD 245

Query: 241 IQAWEYVPLGPFLAKSFATTVSPWVVSIEALRPYFVENP-VQDPVPPAYLHHDDPFTLDI 299
           IQAWEYVPLGPFL KSFA+++SPWVV++EAL P+  ++P  ++P+ P YL  +     DI
Sbjct: 246 IQAWEYVPLGPFLGKSFASSISPWVVTLEALAPFRTKSPKPEEPLLP-YLQCEQDHGFDI 304

Query: 300 NLAVSIRPEGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLRAGDLLGSGTVSGPEEG 359
           +L V I+PEG   + IVC++N+K+LYW + QQLAH TVNGCN+  GD+  SGT+SGPEE 
Sbjct: 305 HLEVGIQPEGKQ-ETIVCRSNYKYLYWNIAQQLAHQTVNGCNINVGDMYASGTISGPEES 363

Query: 360 AYGSMLELSWRGAKEVPV--GSEIRKFLKDGDEVNLSGVCEKNGVRIGFGECRGKVLPAD 417
           ++GSMLEL+W+G K + +  G+E R F++DGD V + G  EK+GVR+GFGE    V+P++
Sbjct: 364 SFGSMLELAWKGTKPIRLDCGAE-RSFIEDGDTVTMRGYAEKDGVRVGFGEVSTAVMPSN 422


Lambda     K      H
   0.319    0.137    0.421 

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: 565
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: 418
Length of database: 425
Length adjustment: 32
Effective length of query: 386
Effective length of database: 393
Effective search space:   151698
Effective search space used:   151698
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 Echvi_2481 Echvi_2481 (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.4198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.2e-180  585.9   0.0   2.5e-180  585.8   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2481  Echvi_2481 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2481  Echvi_2481 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.8   0.0  2.5e-180  2.5e-180       1     419 [.      11     421 ..      11     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 585.8 bits;  conditional E-value: 2.5e-180
                            TIGR01266   1 sfvavaknsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflal 74 
                                          s+v+++knsdf++ nlP+Gvf  ++ +s+rig+aiGd+i+dl ++   g f+   ++  +evf + +ln f+al
  lcl|FitnessBrowser__Cola:Echvi_2481  11 SWVQIPKNSDFTIYNLPFGVFR-NKRLSPRIGMAIGDKIVDLHVLFCEGFFSS--IHLPEEVFLKDSLNEFMAL 81 
                                          8********************9.8899********************9***99..677789************* PP

                            TIGR01266  75 grparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdna 148
                                          g+p+ ++vre +q+ll e++  l+d++  r ++++++ ea+m +P+++Gdytdfyss +hatnvG +fr ++na
  lcl|FitnessBrowser__Cola:Echvi_2481  82 GKPMTRKVREMVQELLLEENTALKDHR-ARGKVMVNRKEAKMLMPVKVGDYTDFYSSKEHATNVGTMFRDPENA 154
                                          **********************99976.58899***************************************** PP

                            TIGR01266 149 llPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpieka 222
                                          l+Pn+khlPvgyhGrass+v sGt+++rP+Gq ka++a++P+fgp+++ld+ele+af  +++ ++G+++  + a
  lcl|FitnessBrowser__Cola:Echvi_2481 155 LMPNWKHLPVGYHGRASSIVPSGTPIHRPKGQFKAPDAEKPSFGPSRRLDFELEMAFITSNPTKMGTSIRTQEA 228
                                          ************************************************************************** PP

                            TIGR01266 223 eehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpylredrad 296
                                          eehifG+vl+ndwsardiqaweyvPlGPfl+ksfa+++sPwvv++eal Pfr++   P+ ++ +lpyl+ + +d
  lcl|FitnessBrowser__Cola:Echvi_2481 229 EEHIFGFVLFNDWSARDIQAWEYVPLGPFLGKSFASSISPWVVTLEALAPFRTK--SPKPEEPLLPYLQCE-QD 299
                                          ******************************************************..99999*******999.89 PP

                            TIGR01266 297 tafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllels 370
                                            fdi+lev +++eG +++++++rsn k lyw ++qqlah +vnGcn++ Gd+++sGtisG+ee +fGs+lel+
  lcl|FitnessBrowser__Cola:Echvi_2481 300 HGFDIHLEVGIQPEG-KQETIVCRSNYKYLYWNIAQQLAHQTVNGCNINVGDMYASGTISGPEESSFGSMLELA 372
                                          99*************.899******************************************************* PP

                            TIGR01266 371 akGkkevkladgetrkfledGdevilrgvckkeGvrvGfGecaGkvlpa 419
                                          +kG+k+++l  g +r f+edGd+v +rg ++k+GvrvGfGe    v+p+
  lcl|FitnessBrowser__Cola:Echvi_2481 373 WKGTKPIRLDCGAERSFIEDGDTVTMRGYAEKDGVRVGFGEVSTAVMPS 421
                                          *******************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (425 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: 7.77
//
[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