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.5590.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 0.00s 00:00:00.01 Elapsed: 00:00:00.08
# Mc/sec: 2.07
//
[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