Alignments for a candidate for fahA in Novosphingobium aromaticivorans DSM 12444

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Novosphingobium aromaticivorans DSM 12444

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_011446105.1 SARO_RS12395 fumarylacetoacetase

Query= SwissProt::P16930
         (419 letters)



>NCBI__GCF_000013325.1:WP_011446105.1
          Length = 431

 Score =  350 bits (897), Expect = e-101
 Identities = 199/427 (46%), Positives = 254/427 (59%), Gaps = 25/427 (5%)

Query: 2   SFIPVA-EDSDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQD 60
           S++P A   +DFP+ NLP+GVF+  G+ RPRIG AIGD +LDL  +  L    VL     
Sbjct: 16  SWVPSALGHADFPVQNLPFGVFAPAGE-RPRIGTAIGDCVLDLCAVGALLPPEVLP---- 70

Query: 61  VFNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPAT 120
           +   P LN+ M   +      R  L  LLS    R   +  L   A +      M LP  
Sbjct: 71  LLELPELNALMAAPRVVKTALRHRLSELLSDDAHRPMVEPALHDAACVE-----MLLPMR 125

Query: 121 IGDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQM 180
           IGDYTDFY    HATN+G +FR  +N L+PN+ H+P+GYHGRASS+  SG P+ RP GQ 
Sbjct: 126 IGDYTDFYVGIHHATNIGKLFRP-DNPLLPNYKHVPIGYHGRASSIRQSGVPVARPRGQR 184

Query: 181 KPDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQ 240
           + +D+  PV+G C  LD ELE+  ++  GN LG  IPI++A EHI G+ L+NDWSARDIQ
Sbjct: 185 RANDADVPVFGPCTRLDYELELGVWISEGNALGTTIPIAEAGEHIAGLCLLNDWSARDIQ 244

Query: 241 KWEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAV---PNPKQDPRPLPYLCHDE----PY 293
            WEY PLGPFL K+F TT+SPWVV  +AL PF +   P P  DP PLPYL  DE      
Sbjct: 245 AWEYQPLGPFLAKNFHTTISPWVVTAEALAPFRIAQPPRPLGDPDPLPYL-RDEADRMAG 303

Query: 294 TFDINLSVNLKGE----GMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASG 349
            F I LSV L  E    G      + +     MYWT+ Q +THH+ NGC L  GDLL +G
Sbjct: 304 AFAIELSVWLTSEQMRAGRYPPLRLSRGPASNMYWTIAQMVTHHASNGCGLNSGDLLGTG 363

Query: 350 TISGPEPENFGSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYR-IGFGQC 408
           TISG E  + GS++E+S  G  P++L  G+TR FLLDGDE+  +      G   IGFG+C
Sbjct: 364 TISGTEQGSKGSLIEISEGGRVPVELPTGETRTFLLDGDEISFSATATAPGRAPIGFGEC 423

Query: 409 AGKVLPA 415
              + PA
Sbjct: 424 RAVIRPA 430


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: 630
Number of extensions: 45
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: 431
Length adjustment: 32
Effective length of query: 387
Effective length of database: 399
Effective search space:   154413
Effective search space used:   154413
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_011446105.1 SARO_RS12395 (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.30197.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.6e-162  524.8   0.0   8.7e-162  524.7   0.0    1.0  1  lcl|NCBI__GCF_000013325.1:WP_011446105.1  SARO_RS12395 fumarylacetoacetase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011446105.1  SARO_RS12395 fumarylacetoacetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  524.7   0.0  8.7e-162  8.7e-162       1     419 [.      16     430 ..      16     431 .] 0.95

  Alignments for each domain:
  == domain 1  score: 524.7 bits;  conditional E-value: 8.7e-162
                                 TIGR01266   1 sfvavak.nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkestl 68 
                                               s+v++a  ++dfp+qnlP+Gvf+  a+ ++rig aiGd +ldl ++ a  l+      e +  ++   l
  lcl|NCBI__GCF_000013325.1:WP_011446105.1  16 SWVPSALgHADFPVQNLPFGVFA-PAGERPRIGTAIGDCVLDLCAVGA--LLPP----EVLPLLELPEL 77 
                                               89999988**************9.8999***************99988..4444....4556777789* PP

                                 TIGR01266  69 naflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhatn 137
                                               na++a +r +++++r+rl +lls++a++      + + al+ +a ++m lP++iGdytdfy++i+hatn
  lcl|NCBI__GCF_000013325.1:WP_011446105.1  78 NALMAAPRVVKTALRHRLSELLSDDAHR-----PMVEPALHDAACVEMLLPMRIGDYTDFYVGIHHATN 141
                                               ***********************66655.....677889****************************** PP

                                 TIGR01266 138 vGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaff 206
                                               +G+lfr +dn+llPnykh+P+gyhGrass++ sG ++ rP Gq +a++a++Pvfgpc +ld+elel+++
  lcl|NCBI__GCF_000013325.1:WP_011446105.1 142 IGKLFR-PDNPLLPNYKHVPIGYHGRASSIRQSGVPVARPRGQRRANDADVPVFGPCTRLDYELELGVW 209
                                               ******.************************************************************** PP

                                 TIGR01266 207 vgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfrv 275
                                               ++++n+lG+++pi  a ehi+G++llndwsardiqawey+PlGPflak+f tt+sPwvv++eal Pfr+
  lcl|NCBI__GCF_000013325.1:WP_011446105.1 210 ISEGNALGTTIPIAEAGEHIAGLCLLNDWSARDIQAWEYQPLGPFLAKNFHTTISPWVVTAEALAPFRI 278
                                               ********************************************************************* PP

                                 TIGR01266 276 aq.lePeqdpkplpylredr..adtafdielevslkteGlae....aavisrsnakslywtlkqqlahh 337
                                               aq  +P +dp plpylr++      af iel+v l++e ++     + ++sr  a ++ywt++q+++hh
  lcl|NCBI__GCF_000013325.1:WP_011446105.1 279 AQpPRPLGDPDPLPYLRDEAdrMAGAFAIELSVWLTSEQMRAgrypPLRLSRGPASNMYWTIAQMVTHH 347
                                               *989*************986325679***********99988788899********************* PP

                                 TIGR01266 338 svnGcnlraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvr 406
                                               + nGc l++Gdllg+GtisG+e+++ Gsl+e+s +G+ +v+l  getr+fl dGde+ +++++   G  
  lcl|NCBI__GCF_000013325.1:WP_011446105.1 348 ASNGCGLNSGDLLGTGTISGTEQGSKGSLIEISEGGRVPVELPTGETRTFLLDGDEISFSATATAPGRA 416
                                               *******************************************************************99 PP

                                 TIGR01266 407 .vGfGecaGkvlpa 419
                                                +GfGec+  + pa
  lcl|NCBI__GCF_000013325.1:WP_011446105.1 417 pIGFGECRAVIRPA 430
                                               9*******998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (431 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.49
//
[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