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; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_038211577.1 Q392_RS20155 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>NCBI__GCF_000745855.1:WP_038211577.1
          Length = 443

 Score =  358 bits (919), Expect = e-103
 Identities = 202/424 (47%), Positives = 259/424 (61%), Gaps = 21/424 (4%)

Query: 7   AEDSDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKH--LFTGPVLSKHQDVFN 63
           AE SDFPI NLP+ VF  +G     R GVAIGDQ+LDL  +    L  G      Q    
Sbjct: 22  AEGSDFPIQNLPFSVFRCKGSQEAFRGGVAIGDQVLDLGALAGAGLLDGAAQQAAQAAV- 80

Query: 64  QPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATIGD 123
           QP LN+   LG  AW+  R  +  LL    A+   DT +R C  + QA     LPA +GD
Sbjct: 81  QPELNALFALGAGAWRALRHGVFALLKEGAAQA--DT-VRAC-LVPQAEVEHALPARVGD 136

Query: 124 YTDFYSSRQHATNVG-IMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKP 182
           YTDFY+S  HA N+  +M  D +  + PN+  LP+ YHGRAS++ VSG   RRPMGQ  P
Sbjct: 137 YTDFYTSLDHALNITRLMIPDGD--VTPNFRWLPIAYHGRASTLGVSGQRFRRPMGQALP 194

Query: 183 DDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKW 242
              + PVY  C  LD ELE+A +VG GN  GEPIP+++A EHIFG+ L+NDWSARDIQ W
Sbjct: 195 PGGRTPVYQPCAKLDYELELAIWVGTGNAAGEPIPLARAEEHIFGIGLLNDWSARDIQMW 254

Query: 243 EYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQ--DPRPLPYL---CHDEPYTFDI 297
           E  PLGPFL K+F TTVSPW+V M+AL P+  P P+   DP+PL YL           DI
Sbjct: 255 EMAPLGPFLAKNFATTVSPWIVTMEALAPYRTPFPRPAGDPQPLAYLDDAAQRAAGGIDI 314

Query: 298 NLSVNLKGE----GMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISG 353
            L V L+ E    G      +  ++F++ YWT  Q + HH+V GC L+PGDL  SGT+SG
Sbjct: 315 RLEVWLESEQARRGAKGPTRLSATSFRHQYWTPAQMVAHHTVGGCALQPGDLFGSGTVSG 374

Query: 354 PEPENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGY-RIGFGQCAGKV 412
           P     G+++EL+  G  P+ L  G+ R FL DGD VI+ G+C+G G+ RIGFG+  G+V
Sbjct: 375 PGAGEAGAIIELARGGQAPVALSTGERRAFLEDGDAVILRGWCEGPGHARIGFGESRGQV 434

Query: 413 LPAL 416
           LPA+
Sbjct: 435 LPAI 438


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: 599
Number of extensions: 27
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: 419
Length of database: 443
Length adjustment: 32
Effective length of query: 387
Effective length of database: 411
Effective search space:   159057
Effective search space used:   159057
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 WP_038211577.1 Q392_RS20155 (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.1176709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-158  512.7   0.0   4.2e-158  512.5   0.0    1.0  1  NCBI__GCF_000745855.1:WP_038211577.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000745855.1:WP_038211577.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.5   0.0  4.2e-158  4.2e-158       1     419 [.      15     437 ..      15     438 .. 0.95

  Alignments for each domain:
  == domain 1  score: 512.5 bits;  conditional E-value: 4.2e-158
                             TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkad.ssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlna 70 
                                           s+v++a+   sdfp+qnlP+ vf +k +    r gvaiGdq+ldl ++a agl++g a+++++++  +  lna
  NCBI__GCF_000745855.1:WP_038211577.1  15 SWVDSANaeGSDFPIQNLPFSVFRCKGSqEAFRGGVAIGDQVLDLGALAGAGLLDG-AAQQAAQAAVQPELNA 86 
                                           7998877558*************988651566899*********************.788888889999**** PP

                             TIGR01266  71 flalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfr 143
                                           ++alg  a++++r+ +  ll e a++    a+  +  l++qae++  lPa++Gdytdfy+s+ ha n+  l+ 
  NCBI__GCF_000745855.1:WP_038211577.1  87 LFALGAGAWRALRHGVFALLKEGAAQ----ADTVRACLVPQAEVEHALPARVGDYTDFYTSLDHALNITRLMI 155
                                           ********************977766....7788899**********************************99 PP

                             TIGR01266 144 gkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGea 216
                                            +d  + Pn+++lP++yhGras++ vsG   rrP+Gq ++++ ++Pv+ pc+kld+elela++vgt+n+ Ge+
  NCBI__GCF_000745855.1:WP_038211577.1 156 -PDGDVTPNFRWLPIAYHGRASTLGVSGQRFRRPMGQALPPGGRTPVYQPCAKLDYELELAIWVGTGNAAGEP 227
                                           .************************************************************************ PP

                             TIGR01266 217 vpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpy 289
                                           +p+ +aeehifG+ llndwsardiq we  PlGPflak+fattvsPw+v++eal P+r++  +P +dp+pl+y
  NCBI__GCF_000745855.1:WP_038211577.1 228 IPLARAEEHIFGIGLLNDWSARDIQMWEMAPLGPFLAKNFATTVSPWIVTMEALAPYRTPFPRPAGDPQPLAY 300
                                           ************************************************************************* PP

                             TIGR01266 290 lredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtis 356
                                           l +    a   +di lev l++e  ++    ++++s + +++ ywt +q++ahh+v Gc l++Gdl+gsGt+s
  NCBI__GCF_000745855.1:WP_038211577.1 301 LDDAAqrAAGGIDIRLEVWLESEQARRgakgPTRLSATSFRHQYWTPAQMVAHHTVGGCALQPGDLFGSGTVS 373
                                           *99763367789********99866555666****************************************** PP

                             TIGR01266 357 GkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                           G+  ++ G+++el+ +G+ +v l+ ge r fledGd vilrg c+  G+  +GfGe +G+vlpa
  NCBI__GCF_000745855.1:WP_038211577.1 374 GPGAGEAGAIIELARGGQAPVALSTGERRAFLEDGDAVILRGWCEGPGHArIGFGESRGQVLPA 437
                                           ************************************************977************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (443 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: 13.07
//
[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