Alignments for a candidate for fahA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Pseudomonas simiae WCS417

Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate GFF990 PS417_05020 fumarylacetoacetase

Query= BRENDA::Q94272
         (418 letters)



>FitnessBrowser__WCS417:GFF990
          Length = 428

 Score =  364 bits (934), Expect = e-105
 Identities = 204/419 (48%), Positives = 266/419 (63%), Gaps = 20/419 (4%)

Query: 10  NSDFPIQNLPYGVFSTKADSSRHIGVAIGDQILNLAEIANLFDGPQLKAHQDVFKQSTLN 69
           ++DFP+QNLP GVFS    + R  GVAIGD IL+L    + FDG   +A +       LN
Sbjct: 17  HTDFPLQNLPLGVFSINGSAPR-AGVAIGDSILDLQAAIDEFDGEARRAIEAT-AGGQLN 74

Query: 70  AFMALPRPAWLEARARIQQLLSEDCAVLRDNAHLRSRALVAQSDATMHLPAQIGDYTDFY 129
           AF AL R   +  R R+ +LL+E   +    A +  RA    +D  MH+PAQI DYTDFY
Sbjct: 75  AFFALGRGPRVALRERLLELLAEGSTLHTREAQVLHRA----ADCQMHVPAQINDYTDFY 130

Query: 130 SSIHHATNVGIMFRGKENALMPNWKWLPVGYHGRASSIVVSGTDLKRPVGQTKAPDAEVP 189
             I HA NVG +FR  +N L+PN+K++P+GYHGRAS+I  SGTD++RP GQT       P
Sbjct: 131 VGIEHAQNVGKLFR-PDNPLLPNYKYVPIGYHGRASTIRTSGTDVRRPKGQTLPAGQSEP 189

Query: 190 SFGPSKLMDFELEMAFFVGGPENELGTRVPIEKAEDRIFGVVLMNDWSARDIQAWEYVPL 249
           +FGP   +D+ELE+  ++G   NE+G  + I  A D I G  L+NDWSARDIQAWEY PL
Sbjct: 190 TFGPCARLDYELELGIWIG-QGNEMGDSIAIGDAADHIAGFCLLNDWSARDIQAWEYQPL 248

Query: 250 GPFLAKSFATTVSPWVVSIEALRPYFVENPVQ---DPVPPAYL---HHDDPFTLDINLAV 303
           GPFL+KSF TT+SPWVV+ EAL P+    P +   DP P +YL          LDI L V
Sbjct: 249 GPFLSKSFITTISPWVVTAEALEPFRKAQPARPEGDPQPLSYLLDKRDQAAGALDIELEV 308

Query: 304 SIRP----EGDAVDHIVCKTNFKHLYWTLKQQLAHHTVNGCNLRAGDLLGSGTVSGPEEG 359
            +      E +   H +  +N  H+YWT+ Q +AHH+VNGC L+AGDL GSGT+SGP+ G
Sbjct: 309 LLTTAAMREQNLPAHRLALSNSLHMYWTVAQLVAHHSVNGCQLQAGDLFGSGTLSGPQAG 368

Query: 360 AYGSMLELSWRGAKEVPVGS-EIRKFLKDGDEVNLSGVCEKNG-VRIGFGECRGKVLPA 416
            +GS+LE++  G K V + S E+RKFL+DGDE+ L   C + G   IGFGECRG V+ A
Sbjct: 369 QFGSLLEMTEGGKKPVELPSGEVRKFLEDGDEIILRARCNREGFASIGFGECRGTVIAA 427


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: 548
Number of extensions: 30
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: 428
Length adjustment: 32
Effective length of query: 386
Effective length of database: 396
Effective search space:   152856
Effective search space used:   152856
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 GFF990 PS417_05020 (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.30986.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.9e-190  618.5   0.0   3.3e-190  618.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF990  PS417_05020 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF990  PS417_05020 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.3   0.0  3.3e-190  3.3e-190       1     419 [.       9     427 ..       9     428 .] 0.97

  Alignments for each domain:
  == domain 1  score: 618.3 bits;  conditional E-value: 3.3e-190
                          TIGR01266   1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestlnaflalg 75 
                                        s+va+a+ ++dfplqnlP+Gvfs  ++s +r gvaiGd+ildl+++ +   f+g  ++++ e++ ++ lnaf+alg
  lcl|FitnessBrowser__WCS417:GFF990   9 SWVASANgHTDFPLQNLPLGVFS-INGSAPRAGVAIGDSILDLQAAID--EFDG-EARRAIEATAGGQLNAFFALG 80 
                                        8******9***************.7899****************9999..9***.8899***************** PP

                          TIGR01266  76 rparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatnvGilfrgkdnallP 151
                                        r  r+++rerl++ll+e +       +   ++l+ +a+++mh+Paqi dytdfy++i+ha+nvG+lfr +dn+llP
  lcl|FitnessBrowser__WCS417:GFF990  81 RGPRVALRERLLELLAEGSTL----HTREAQVLHRAADCQMHVPAQINDYTDFYVGIEHAQNVGKLFR-PDNPLLP 151
                                        ****************77766....4556789************************************.******* PP

                          TIGR01266 152 nykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaffvgtenelGeavpiekaeehif 227
                                        nyk++P+gyhGras++++sGt++rrP+Gq+++++ +eP+fgpc++ld+elel++++g++ne+G+++ i  a++hi+
  lcl|FitnessBrowser__WCS417:GFF990 152 NYKYVPIGYHGRASTIRTSGTDVRRPKGQTLPAGQSEPTFGPCARLDYELELGIWIGQGNEMGDSIAIGDAADHIA 227
                                        **************************************************************************** PP

                          TIGR01266 228 GvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrvaq.lePeqdpkplpylredr..adtafd 300
                                        G++llndwsardiqawey+PlGPfl+ksf+tt+sPwvv++ealePfr+aq ++Pe+dp+pl+yl ++r  a  a+d
  lcl|FitnessBrowser__WCS417:GFF990 228 GFCLLNDWSARDIQAWEYQPLGPFLSKSFITTISPWVVTAEALEPFRKAQpARPEGDPQPLSYLLDKRdqAAGALD 303
                                        **************************************************9**************999556689** PP

                          TIGR01266 301 ielevslkteGlae....aavisrsnakslywtlkqqlahhsvnGcnlraGdllgsGtisGkeeeafGsllelsak 372
                                        ielev l+t+ ++e    a++++ sn++++ywt++q +ahhsvnGc+l+aGdl+gsGt+sG++ ++fGslle++ +
  lcl|FitnessBrowser__WCS417:GFF990 304 IELEVLLTTAAMREqnlpAHRLALSNSLHMYWTVAQLVAHHSVNGCQLQAGDLFGSGTLSGPQAGQFGSLLEMTEG 379
                                        *************9889889******************************************************** PP

                          TIGR01266 373 GkkevkladgetrkfledGdevilrgvckkeGvr.vGfGecaGkvlpa 419
                                        Gkk+v+l +ge+rkfledGde+ilr++c++eG   +GfGec+G+v++a
  lcl|FitnessBrowser__WCS417:GFF990 380 GKKPVELPSGEVRKFLEDGDEIILRARCNREGFAsIGFGECRGTVIAA 427
                                        ********************************988**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (428 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: 11.33
//
[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