Alignments for a candidate for fahA in Rhodopseudomonas palustris CGA009

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Rhodopseudomonas palustris CGA009

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_011160202.1 TX73_RS23885 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>NCBI__GCF_000195775.1:WP_011160202.1
          Length = 421

 Score =  466 bits (1199), Expect = e-136
 Identities = 220/414 (53%), Positives = 283/414 (68%), Gaps = 3/414 (0%)

Query: 2   SFIPVAEDSDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQDV 61
           SF+ V  +SDFPI NLPYGV ST  DP PR+GVAIGD +LDL+ ++      +L   +DV
Sbjct: 10  SFVDVKPESDFPIQNLPYGVVSTADDPAPRVGVAIGDFVLDLAALQ---AAKLLDLPEDV 66

Query: 62  FNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATI 121
           F Q ++N+FM LG   W+  R  +  LL      LRD  ELR  A +  +   +HLP  +
Sbjct: 67  FTQSSINAFMALGPNVWRRTRARINALLRHDNPELRDHAELRAKALLPMSQVKLHLPLRV 126

Query: 122 GDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMK 181
             +TDFYSS++HATNVG MFRDK N L+PNWLH+P+GY+GRAS+VVVSGT I RP GQ+K
Sbjct: 127 AGFTDFYSSKEHATNVGTMFRDKTNPLLPNWLHIPIGYNGRASTVVVSGTQIHRPRGQLK 186

Query: 182 PDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQK 241
           P  ++ P +G CK LD ELE+   VG  + +G  +   +A E IFG  L+NDWSARDIQ+
Sbjct: 187 PPSAELPSFGPCKRLDFELEIGVVVGQSSAMGTMLTEQQAEEMIFGFTLLNDWSARDIQQ 246

Query: 242 WEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINLSV 301
           WEYVPLGPF  K+F T++SPW+V  +AL PF V  P QDP PLPYL       +D+ L V
Sbjct: 247 WEYVPLGPFQAKAFATSISPWIVTREALEPFRVAGPVQDPAPLPYLQQKGANNYDMALEV 306

Query: 302 NLKGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENFGS 361
            L+   M Q A I  +NFKYMYW+ +QQL HH+ +GC +  GDLL SGT+SGPE +  GS
Sbjct: 307 ALRTPAMQQPARISATNFKYMYWSSVQQLVHHASSGCAMSVGDLLGSGTVSGPEKDQLGS 366

Query: 362 MLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415
           +LELSW GT+P+ L  G+ R FL DGD +++ G+CQGDGYR+GFG+  G VL A
Sbjct: 367 LLELSWNGTEPLQLPGGELRGFLEDGDSLVMRGWCQGDGYRVGFGEVEGTVLAA 420


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: 607
Number of extensions: 21
Number of successful extensions: 2
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: 421
Length adjustment: 32
Effective length of query: 387
Effective length of database: 389
Effective search space:   150543
Effective search space used:   150543
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_011160202.1 TX73_RS23885 (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.9660.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-176  572.9   0.0   2.2e-176  572.8   0.0    1.0  1  lcl|NCBI__GCF_000195775.1:WP_011160202.1  TX73_RS23885 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011160202.1  TX73_RS23885 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.8   0.0  2.2e-176  2.2e-176       1     419 [.      10     420 ..      10     421 .] 0.99

  Alignments for each domain:
  == domain 1  score: 572.8 bits;  conditional E-value: 2.2e-176
                                 TIGR01266   1 sfvavaknsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestln 69 
                                               sfv+v  +sdfp+qnlPyGv+st  d+ +r+gvaiGd +ldl++++aa l++       ++vf +s++n
  lcl|NCBI__GCF_000195775.1:WP_011160202.1  10 SFVDVKPESDFPIQNLPYGVVSTADDPAPRVGVAIGDFVLDLAALQAAKLLDL-----PEDVFTQSSIN 73 
                                               89*********************************************877776.....689******** PP

                                 TIGR01266  70 aflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnv 138
                                               af+alg  ++++ r+r+  ll +++  lrd+a+lr +all++++++ hlP ++  +tdfyss +hatnv
  lcl|NCBI__GCF_000195775.1:WP_011160202.1  74 AFMALGPNVWRRTRARINALLRHDNPELRDHAELRAKALLPMSQVKLHLPLRVAGFTDFYSSKEHATNV 142
                                               ********************************************************************* PP

                                 TIGR01266 139 GilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffv 207
                                               G +fr k n+llPn+ h+P+gy Gras+vvvsGt+++rP Gq+k++ a++P+fgpck+ld+ele+++ v
  lcl|NCBI__GCF_000195775.1:WP_011160202.1 143 GTMFRDKTNPLLPNWLHIPIGYNGRASTVVVSGTQIHRPRGQLKPPSAELPSFGPCKRLDFELEIGVVV 211
                                               ********************************************************************* PP

                                 TIGR01266 208 gtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrva 276
                                               g++ ++G+ +  ++aee ifG+ llndwsardiq+weyvPlGPf ak+fat++sPw+v+ ealePfrva
  lcl|NCBI__GCF_000195775.1:WP_011160202.1 212 GQSSAMGTMLTEQQAEEMIFGFTLLNDWSARDIQQWEYVPLGPFQAKAFATSISPWIVTREALEPFRVA 280
                                               ********************************************************************9 PP

                                 TIGR01266 277 qlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcnlr 345
                                                  P+qdp plpyl+++     +d+ lev l+t  ++++a+is +n+k +yw+  qql hh+ +Gc + 
  lcl|NCBI__GCF_000195775.1:WP_011160202.1 281 --GPVQDPAPLPYLQQK-GANNYDMALEVALRTPAMQQPARISATNFKYMYWSSVQQLVHHASSGCAMS 346
                                               ..9************99.8889*********************************************** PP

                                 TIGR01266 346 aGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGecaG 414
                                                GdllgsGt+sG+e+++ Gsllels++G+++++l  ge r fledGd +++rg c+ +G+rvGfGe  G
  lcl|NCBI__GCF_000195775.1:WP_011160202.1 347 VGDLLGSGTVSGPEKDQLGSLLELSWNGTEPLQLPGGELRGFLEDGDSLVMRGWCQGDGYRVGFGEVEG 415
                                               ********************************************************************* PP

                                 TIGR01266 415 kvlpa 419
                                               +vl+a
  lcl|NCBI__GCF_000195775.1:WP_011160202.1 416 TVLAA 420
                                               ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (421 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: 00:00:00.02
# Mc/sec: 8.12
//
[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