Alignments for a candidate for fahA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Phaeobacter inhibens BS107

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate GFF43 PGA1_c00430 fumarylacetoacetase Fah

Query= BRENDA::Q8RW90
         (421 letters)



>FitnessBrowser__Phaeo:GFF43
          Length = 418

 Score =  375 bits (963), Expect = e-108
 Identities = 197/420 (46%), Positives = 263/420 (62%), Gaps = 14/420 (3%)

Query: 1   MALLKSFID-VGSDSH-FPIQNLPYGVFKPESNSTPRPAVAIGDLVLDLSAISEAGLFDG 58
           M L+KS++    S +H FP+ NLPYGVF  +S+  PR  VAIGD++LD+ A  E GL   
Sbjct: 1   MPLMKSWVSSANSTAHPFPLNNLPYGVFSVDSDD-PRCGVAIGDMILDMQAAEETGLIQ- 58

Query: 59  LILKDADCFLQPNLNKFLAMGRPAWKEARSTLQRILSSNEPILRDNDVLRRKSFHQMSKV 118
             L D   F  P  N  +  G   W   R  L  +LS         + L   +    S  
Sbjct: 59  --LGDVPLFDVPYWNDLMEEGPAVWAALRDRLTALLSEGAAEQEKVEPLLVAA----SAA 112

Query: 119 EMIVPMVIGDYTDFFASMHHAKNCGLMFRGPENAINPNWFRLPIAYHGRASSIVISGTDI 178
           E+ +P  + +YTDF+A  +HA N G MFRGPENA+ PNW  +PI Y+GRASS+V SGTD+
Sbjct: 113 ELHMPFAVSEYTDFYAGKNHAFNVGTMFRGPENALPPNWLHIPIGYNGRASSVVASGTDV 172

Query: 179 IRPRGQGHPQGNSEPYFGPSKKLDFELEMAAVVGPGNELGKPIDVNNAADHIFGLLLMND 238
            RP GQ     + +P + P  + D ELEM A+VG  +E   PI V  A DHIFG +L+ND
Sbjct: 173 RRPWGQLKGPNDDKPRWAPCARFDIELEMGAIVGTPSE--GPITVQEADDHIFGYVLLND 230

Query: 239 WSARDIQAWEYVPLGPFLGKSFGTTISPWIVTLDALEPFGCQAPKQDPPPLPYLAEKESV 298
           WSARDIQAWEY PLGPF  K+   TISPWIVT  ALEPF C  P+++   L +L +   +
Sbjct: 231 WSARDIQAWEYQPLGPFQAKATANTISPWIVTKAALEPFRCDTPEREVELLDHLKDCGPM 290

Query: 299 NYDISLEVQLKPSGRDDSCVITKSNFQNLYWTITQQLAHHTVNGCNLRPGDLLGTGTISG 358
            YDI LEV + P G+ ++  I ++N++ +Y++  QQLAHH  +GC +  GDLLG+GTISG
Sbjct: 291 LYDIDLEVTMAPEGK-EATTIARTNYKEMYYSAAQQLAHHATSGCPMNAGDLLGSGTISG 349

Query: 359 PEPDSYGCLLELTWNGQKPLSLN-GTTQTFLEDGDQVTFSGVCKGDGYNVGFGTCTGKIV 417
              DS G LLEL+W G++PL+L+ G  ++F+ DGD +T  G  KGDGY +GFG CTG ++
Sbjct: 350 STKDSRGSLLELSWGGKEPLTLDTGEERSFIADGDTLTLKGAAKGDGYTIGFGDCTGTVL 409


Lambda     K      H
   0.319    0.139    0.434 

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: 592
Number of extensions: 28
Number of successful extensions: 6
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: 421
Length of database: 418
Length adjustment: 32
Effective length of query: 389
Effective length of database: 386
Effective search space:   150154
Effective search space used:   150154
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF43 PGA1_c00430 (fumarylacetoacetase Fah)
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.10116.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.1e-153  496.5   0.0   3.6e-153  496.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF43  PGA1_c00430 fumarylacetoacetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF43  PGA1_c00430 fumarylacetoacetase Fah
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.3   0.0  3.6e-153  3.6e-153       1     420 []       6     412 ..       6     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 496.3 bits;  conditional E-value: 3.6e-153
                        TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalgr 76 
                                      s+v++a+    +fpl+nlPyGvfs   + ++r+gvaiGd ild++++ ++gl +          f+    n ++  g 
  lcl|FitnessBrowser__Phaeo:GFF43   6 SWVSSANstAHPFPLNNLPYGVFSV-DSDDPRCGVAIGDMILDMQAAEETGLIQL----GDVPLFDVPYWNDLMEEGP 78 
                                      89*999955569************5.55689******************888766....567899************* PP

                        TIGR01266  77 parkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallPnyk 154
                                      +++ ++r+rl  llse a+     +++ + +l+a++ a+ h+P  + +ytdfy++ +ha nvG +frg++nal Pn+ 
  lcl|FitnessBrowser__Phaeo:GFF43  79 AVWAALRDRLTALLSEGAAE----QEKVEPLLVAASAAELHMPFAVSEYTDFYAGKNHAFNVGTMFRGPENALPPNWL 152
                                      ***************66665....66777899********************************************** PP

                        TIGR01266 155 hlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaeehifGvvll 232
                                      h+P+gy Grassvv sGt++rrP Gq+k +n ++P ++pc+++d+ele++  vgt+ e   ++ ++ a++hifG vll
  lcl|FitnessBrowser__Phaeo:GFF43 153 HIPIGYNGRASSVVASGTDVRRPWGQLKGPNDDKPRWAPCARFDIELEMGAIVGTPSE--GPITVQEADDHIFGYVLL 228
                                      *******************************************************997..69**************** PP

                        TIGR01266 233 ndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaqlePeqdpkplpylredradtafdielevslkte 310
                                      ndwsardiqawey+PlGPf ak+ a t+sPw+v+  alePfr     Pe++ ++l +l++   ++ +di+lev++ +e
  lcl|FitnessBrowser__Phaeo:GFF43 229 NDWSARDIQAWEYQPLGPFQAKATANTISPWIVTKAALEPFRCD--TPEREVELLDHLKDC-GPMLYDIDLEVTMAPE 303
                                      *******************************************9..9***********998.9*************** PP

                        TIGR01266 311 GlaeaavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfl 388
                                      G +ea++i+r+n k++y++ +qqlahh+ +Gc ++aGdllgsGtisG+ +++ Gsllels++Gk+++ l  ge+r f+
  lcl|FitnessBrowser__Phaeo:GFF43 304 G-KEATTIARTNYKEMYYSAAQQLAHHATSGCPMNAGDLLGSGTISGSTKDSRGSLLELSWGGKEPLTLDTGEERSFI 380
                                      *.99************************************************************************** PP

                        TIGR01266 389 edGdevilrgvckkeGvrvGfGecaGkvlpal 420
                                       dGd++ l+g +k +G+++GfG+c+G+vl+al
  lcl|FitnessBrowser__Phaeo:GFF43 381 ADGDTLTLKGAAKGDGYTIGFGDCTGTVLAAL 412
                                      *****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (418 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: 10.99
//
[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