Alignments for a candidate for fahA in Derxia gummosa DSM 723

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Derxia gummosa DSM 723

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_028311730.1 H566_RS0112650 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>NCBI__GCF_000482785.1:WP_028311730.1
          Length = 442

 Score =  375 bits (962), Expect = e-108
 Identities = 208/427 (48%), Positives = 266/427 (62%), Gaps = 17/427 (3%)

Query: 2   SFIPVAED--SDFPIHNLPYGVFSTRGDPRP-RIGVAIGDQILDLSIIKHLFTGPVLSKH 58
           S++  A D  SDFPI NLP+G     G  +P RIGVAIGDQ LDL++   L  G      
Sbjct: 15  SWVASANDPASDFPIQNLPFGRLRRAGSEQPWRIGVAIGDQALDLALA--LAAGGWSEDE 72

Query: 59  QDVFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLP 118
           Q V  +P     +    AA    R  L+  LS + A           A + QA A   LP
Sbjct: 73  QAVL-RPLARGDLNALMAAGPLPRRLLRGALSRALAEGSPQAGALAGALLPQAEAEFTLP 131

Query: 119 ATIGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMG 178
             IGDYTDFY+   HAT VG +FR  +N L+PN+  +P+GYHGR SS+ VSG   RRP+G
Sbjct: 132 CHIGDYTDFYTGIHHATTVGKLFRP-DNPLLPNYKWVPIGYHGRCSSIGVSGHAFRRPLG 190

Query: 179 QMKPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARD 238
           Q+K  +++ PV    + LD ELE+  FVG  N  GEP+P++ A +H+FG+VL+NDWSARD
Sbjct: 191 QVKTPEAEAPVLAPSRRLDYELELGVFVGAPNAQGEPVPLADAEDHLFGVVLLNDWSARD 250

Query: 239 IQKWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVP--NPKQDPRPLPYLCHDEPY--- 293
           +Q WEY PLGPFL K+F TT+SPW+V MDAL PF VP   P+ +P PLPYL  +      
Sbjct: 251 VQAWEYQPLGPFLSKNFATTISPWIVTMDALAPFRVPFARPEGEPAPLPYLDGESNRARG 310

Query: 294 TFDINLSVNLKGEGMSQA----ATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASG 349
             D++  V ++   M +A    A + +SNF+  +WTM Q L HH+V GCNL+PGDLL SG
Sbjct: 311 ALDLHFEVLIETPRMREAGEAPARLSRSNFRDAWWTMAQMLAHHTVGGCNLQPGDLLGSG 370

Query: 350 TISGPEPENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYR-IGFGQC 408
           T SGP P   GS+LELS  G +P+ L NG+TR FLLDGD V++ G C+  G R IGFG C
Sbjct: 371 TQSGPAPGEGGSLLELSLGGKQPLTLPNGETRSFLLDGDTVLLRGRCEAAGARAIGFGDC 430

Query: 409 AGKVLPA 415
           AG VLPA
Sbjct: 431 AGSVLPA 437


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: 634
Number of extensions: 42
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: 419
Length of database: 442
Length adjustment: 32
Effective length of query: 387
Effective length of database: 410
Effective search space:   158670
Effective search space used:   158670
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_028311730.1 H566_RS0112650 (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.713364.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-164  532.5   0.0   4.2e-164  532.3   0.0    1.0  1  NCBI__GCF_000482785.1:WP_028311730.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000482785.1:WP_028311730.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.3   0.0  4.2e-164  4.2e-164       1     419 [.      15     437 ..      15     438 .. 0.95

  Alignments for each domain:
  == domain 1  score: 532.3 bits;  conditional E-value: 4.2e-164
                             TIGR01266   1 sfvavak..nsdfplqnlPyGvfstk.adssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlna 70 
                                           s+va+a+   sdfp+qnlP+G +    +++  rigvaiGdq+ldl+ ++aag++++   ++ +  + ++ lna
  NCBI__GCF_000482785.1:WP_028311730.1  15 SWVASANdpASDFPIQNLPFGRLRRAgSEQPWRIGVAIGDQALDLALALAAGGWSE-DEQAVLRPLARGDLNA 86 
                                           8*****96679**********998441344459*********************99.77888999999***** PP

                             TIGR01266  71 flalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfr 143
                                           ++a g   r+ +r  l + l+e + +    a     all+qaea+  lP +iGdytdfy++i+hat vG+lfr
  NCBI__GCF_000482785.1:WP_028311730.1  87 LMAAGPLPRRLLRGALSRALAEGSPQ----AGALAGALLPQAEAEFTLPCHIGDYTDFYTGIHHATTVGKLFR 155
                                           *****************999965544....777889************************************* PP

                             TIGR01266 144 gkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGea 216
                                            +dn+llPnyk++P+gyhGr ss+ vsG   rrP Gq+k+++a+ Pv +p+++ld+elel++fvg +n+ Ge+
  NCBI__GCF_000482785.1:WP_028311730.1 156 -PDNPLLPNYKWVPIGYHGRCSSIGVSGHAFRRPLGQVKTPEAEAPVLAPSRRLDYELELGVFVGAPNAQGEP 227
                                           .************************************************************************ PP

                             TIGR01266 217 vpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpy 289
                                           vp+  ae+h+fGvvllndwsard+qawey+PlGPfl+k+fatt+sPw+v+++al Pfrv+ ++Pe++p plpy
  NCBI__GCF_000482785.1:WP_028311730.1 228 VPLADAEDHLFGVVLLNDWSARDVQAWEYQPLGPFLSKNFATTISPWIVTMDALAPFRVPFARPEGEPAPLPY 300
                                           ************************************************************************* PP

                             TIGR01266 290 lredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtis 356
                                           l  +   a  a+d+++ev ++t  ++e    +a++srsn+++ +wt++q+lahh+v Gcnl++GdllgsGt s
  NCBI__GCF_000482785.1:WP_028311730.1 301 LDGESnrARGALDLHFEVLIETPRMREageaPARLSRSNFRDAWWTMAQMLAHHTVGGCNLQPGDLLGSGTQS 373
                                           *85533499***********999888877779***************************************** PP

                             TIGR01266 357 GkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                           G+ +++ Gsllels +Gk+++ l +getr fl dGd+v lrg+c+  G r +GfG+caG vlpa
  NCBI__GCF_000482785.1:WP_028311730.1 374 GPAPGEGGSLLELSLGGKQPLTLPNGETRSFLLDGDTVLLRGRCEAAGARaIGFGDCAGSVLPA 437
                                           ************************************************999************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (442 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.37
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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