Alignments for a candidate for fahA in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Xenophilus azovorans DSM 13620

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_038200417.1 Q392_RS01235 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>NCBI__GCF_000745855.1:WP_038200417.1
          Length = 422

 Score =  363 bits (933), Expect = e-105
 Identities = 213/417 (51%), Positives = 264/417 (63%), Gaps = 32/417 (7%)

Query: 11  SDFPIQNLPYGVFSTKADSSR-HIGVAIGDQILNLAEIANLFDGPQLKAHQDVFKQSTLN 69
           SDFPIQNLP+G F  K       IGVAIGDQ+L+L   A L D               +N
Sbjct: 24  SDFPIQNLPFGRFRRKGSGEAFRIGVAIGDQVLDL-RAAGLVD------------TDDMN 70

Query: 70  AFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQSDATMHLPAQIGDYTDFY 129
           A MA   PA    R  ++  LS+  A         ++ALV Q+D    +P ++GDYTDFY
Sbjct: 71  ALMAAA-PA---GRRALRAKLSDGLAAGSTQQAAWAQALVPQADCEYTVPCRVGDYTDFY 126

Query: 130 SSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGTDLKRPVGQTKAPDAEVP 189
           + IHHAT +G +FR  +  LMPN+KW+P+GYHGRASSIVVSGT  KRP GQTKAPDA  P
Sbjct: 127 TGIHHATTIGKLFR-PDQPLMPNYKWVPIGYHGRASSIVVSGTPFKRPQGQTKAPDAAEP 185

Query: 190 SFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVLMNDWSARDIQAWEYVPL 249
           SFGP K +D+ELE+ F+V G  N LG  V I+ AE  +FGV L NDWSARD+QAWEY PL
Sbjct: 186 SFGPCKRLDYELELGFYV-GQGNALGQPVGIDDAEAHLFGVGLFNDWSARDLQAWEYQPL 244

Query: 250 GPFLAKSFATTVSPWVVSIEALRPYFV--ENPVQDPVPPAYLH---HDDPFTLDINLAV- 303
           GPFLAK+FA+TVSPW+V++EAL P+      P  DP P  YL    + +   LDI L V 
Sbjct: 245 GPFLAKNFASTVSPWIVTMEALAPFRAPFTRPAGDPQPLPYLDGAANREGGQLDITLEVL 304

Query: 304 ----SIRPEGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLRAGDLLGSGTVSGPEEG 359
                +R +G+A   +      +  YWT  Q LAHHTVNGCNL+ GDLLGSGT+SGP   
Sbjct: 305 VQTAKMREQGEAPARLTHGLVKEAAYWTAAQLLAHHTVNGCNLQPGDLLGSGTLSGPTPD 364

Query: 360 AYGSMLELSWRGAKEVPV-GSEIRKFLKDGDEVNLSGVCEKNG-VRIGFGECRGKVL 414
           A GS++EL+  G + + + G E R FL+DGD + L G CE+ G VRIGFGE  G VL
Sbjct: 365 AAGSLMELTLGGKQPITLPGGEQRTFLQDGDTLVLRGWCERAGAVRIGFGEASGTVL 421


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: 551
Number of extensions: 28
Number of successful extensions: 8
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: 422
Length adjustment: 32
Effective length of query: 386
Effective length of database: 390
Effective search space:   150540
Effective search space used:   150540
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 WP_038200417.1 Q392_RS01235 (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.24270.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-158  512.9   0.0   1.3e-157  511.0   0.0    1.7  1  lcl|NCBI__GCF_000745855.1:WP_038200417.1  Q392_RS01235 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038200417.1  Q392_RS01235 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.0   0.0  1.3e-157  1.3e-157       1     418 [.      14     422 .]      14     422 .] 0.94

  Alignments for each domain:
  == domain 1  score: 511.0 bits;  conditional E-value: 1.3e-157
                                 TIGR01266   1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfeglalkehqevfkes 66 
                                               s+v++a+   sdfp+qnlP+G f  k ++   rigvaiGdq+ldl +   agl +              
  lcl|NCBI__GCF_000745855.1:WP_038200417.1  14 SWVESANaaGSDFPIQNLPFGRFRRKgSGEAFRIGVAIGDQVLDLRA---AGLVDT------------D 67 
                                               89999986679************9762456779***********975...466655............5 PP

                                 TIGR01266  67 tlnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirha 135
                                                +na++a + + r+++r++l + l++ + +    +a   +al++qa+++  +P ++Gdytdfy++i+ha
  lcl|NCBI__GCF_000745855.1:WP_038200417.1  68 DMNALMAAAPAGRRALRAKLSDGLAAGSTQ----QAAWAQALVPQADCEYTVPCRVGDYTDFYTGIHHA 132
                                               68********************99955544....677889***************************** PP

                                 TIGR01266 136 tnvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelela 204
                                               t +G+lfr +d +l+Pnyk++P+gyhGrass+vvsGt+ +rP+Gq+ka++a eP+fgpck+ld+elel+
  lcl|NCBI__GCF_000745855.1:WP_038200417.1 133 TTIGKLFR-PDQPLMPNYKWVPIGYHGRASSIVVSGTPFKRPQGQTKAPDAAEPSFGPCKRLDYELELG 200
                                               ********.************************************************************ PP

                                 TIGR01266 205 ffvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePf 273
                                               f+vg++n+lG++v i+ ae h+fGv l+ndwsard+qawey+PlGPflak+fa+tvsPw+v++eal Pf
  lcl|NCBI__GCF_000745855.1:WP_038200417.1 201 FYVGQGNALGQPVGIDDAEAHLFGVGLFNDWSARDLQAWEYQPLGPFLAKNFASTVSPWIVTMEALAPF 269
                                               ********************************************************************* PP

                                 TIGR01266 274 rvaqlePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnaks.lywtlkqqla 335
                                               r + ++P +dp+plpyl      +   +di lev ++t+ ++e    +a++++  +k+  ywt +q la
  lcl|NCBI__GCF_000745855.1:WP_038200417.1 270 RAPFTRPAGDPQPLPYLDGAAnrEGGQLDITLEVLVQTAKMREqgeaPARLTHGLVKEaAYWTAAQLLA 338
                                               *****************7643228899************999988889999999988637********* PP

                                 TIGR01266 336 hhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeG 404
                                               hh+vnGcnl++GdllgsGt+sG+ ++a Gsl+el+ +Gk+++ l  ge+r+fl+dGd+++lrg c++ G
  lcl|NCBI__GCF_000745855.1:WP_038200417.1 339 HHTVNGCNLQPGDLLGSGTLSGPTPDAAGSLMELTLGGKQPITLPGGEQRTFLQDGDTLVLRGWCERAG 407
                                               ********************************************************************* PP

                                 TIGR01266 405 vr.vGfGecaGkvlp 418
                                                + +GfGe  G+vl+
  lcl|NCBI__GCF_000745855.1:WP_038200417.1 408 AVrIGFGEASGTVLA 422
                                               877**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (422 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 3.59
//
[ok]

This GapMind analysis is from Sep 24 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