Alignments for a candidate for fahA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for fahA in Sphingomonas koreensis DSMZ 15582

Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate Ga0059261_1693 Ga0059261_1693 fumarylacetoacetate hydrolase (EC 3.7.1.2)

Query= SwissProt::P16930
         (419 letters)



>FitnessBrowser__Korea:Ga0059261_1693
          Length = 419

 Score =  390 bits (1002), Expect = e-113
 Identities = 204/412 (49%), Positives = 269/412 (65%), Gaps = 16/412 (3%)

Query: 7   AEDSDFPIHNLPYGVFS--TRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQDVFNQ 64
           A D+DFP++NLPYGVFS  TRG   PR GVAIGD+ILD++ ++    G +      +F +
Sbjct: 13  AADTDFPLNNLPYGVFSDATRG---PRCGVAIGDRILDMAALEA--AGLLRLGDVPLFAE 67

Query: 65  PTLNSFMGLGQAAWKEARVFLQNLLSVSQA-RLRDDTELRKCAFISQASATMHLPATIGD 123
           P  N+ M  G A W   R  L  LL+   A R+  +  L     +  A A +HLP  +  
Sbjct: 68  PGWNTLMAQGPAVWGALRAQLIALLAEGAAERVAVEPHL-----VPMAGAQLHLPFRVAG 122

Query: 124 YTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMKPD 183
           YTDFY+SRQHA NVG MFR  ENAL PNWLH+P+GY+GRASSVVVSGT +RRP GQ+K  
Sbjct: 123 YTDFYASRQHAFNVGTMFRGAENALPPNWLHIPIGYNGRASSVVVSGTDVRRPWGQVKGP 182

Query: 184 DSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQKWE 243
           +   P +      D+ELE+   VG G+   +P+ +++A   IFG VL+NDWSARDIQ WE
Sbjct: 183 EDAAPRFAPSARFDIELELGAIVGTGS--SDPLTVAEADAMIFGYVLLNDWSARDIQAWE 240

Query: 244 YVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINLSVNL 303
           Y PLGPF GK+  TT+SPW+V   AL PF    P ++   LPYL    P  +DI+L V L
Sbjct: 241 YQPLGPFQGKATATTISPWIVTAAALEPFRAHGPAREKPLLPYLDEPGPMLYDIDLEVGL 300

Query: 304 KGEGMSQAATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENFGSML 363
             EG +++  I +++++ MY++  QQL HHS  GC +  GDLL +GTISGP+  +FGS+L
Sbjct: 301 TPEGGAESV-ISRTSYREMYYSAAQQLAHHSTAGCRMEVGDLLGTGTISGPDKGSFGSLL 359

Query: 364 ELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQGDGYRIGFGQCAGKVLPA 415
           ELSW G +P+ L  G  R F+ DGD +I+ G C+GDGYRIGFG C+G V+PA
Sbjct: 360 ELSWGGKEPLTLAGGAQRSFVEDGDTLILRGQCRGDGYRIGFGDCSGTVIPA 411


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: 582
Number of extensions: 26
Number of successful extensions: 5
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: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
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 Ga0059261_1693 Ga0059261_1693 (fumarylacetoacetate hydrolase (EC 3.7.1.2))
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.18157.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-155  502.0   0.0   7.4e-155  501.8   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1693  Ga0059261_1693 fumarylacetoaceta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1693  Ga0059261_1693 fumarylacetoacetate hydrolase (EC 3.7.1.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.8   0.0  7.4e-155  7.4e-155       1     419 [.       6     411 ..       6     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 501.8 bits;  conditional E-value: 7.4e-155
                                 TIGR01266   1 sfvavak..nsdfplqnlPyGvfstkadssrrigvaiGdqildlskiaaaglfeglalkehqevfkest 67 
                                               s+va a+  ++dfpl+nlPyGvfs  a+  +r+gvaiGd+ild++++ aagl+           f e  
  lcl|FitnessBrowser__Korea:Ga0059261_1693   6 SWVAAANaaDTDFPLNNLPYGVFS-DATRGPRCGVAIGDRILDMAALEAAGLLRL----GDVPLFAEPG 69 
                                               899998866899************.9999********************999886....56789***** PP

                                 TIGR01266  68 lnaflalgrparkevrerlqkllsesaevlrdnaalrkeallaqaeatmhlPaqiGdytdfyssirhat 136
                                                n+++a g +++ ++r++l  ll+e a+     +   +  l+++a a+ hlP ++  ytdfy+s++ha 
  lcl|FitnessBrowser__Korea:Ga0059261_1693  70 WNTLMAQGPAVWGALRAQLIALLAEGAAE----RVAVEPHLVPMAGAQLHLPFRVAGYTDFYASRQHAF 134
                                               ************************66555....444556799*************************** PP

                                 TIGR01266 137 nvGilfrgkdnallPnykhlPvgyhGrassvvvsGtelrrPvGqikadnakePvfgpckkldlelelaf 205
                                               nvG +frg +nal Pn+ h+P+gy GrassvvvsGt++rrP Gq+k ++   P f+p++++d+elel+ 
  lcl|FitnessBrowser__Korea:Ga0059261_1693 135 NVGTMFRGAENALPPNWLHIPIGYNGRASSVVVSGTDVRRPWGQVKGPEDAAPRFAPSARFDIELELGA 203
                                               ********************************************************************* PP

                                 TIGR01266 206 fvgtenelGeavpiekaeehifGvvllndwsardiqaweyvPlGPflaksfattvsPwvvsiealePfr 274
                                                vgt+ +  +++ +  a+  ifG vllndwsardiqawey+PlGPf +k+ att+sPw+v++ alePfr
  lcl|FitnessBrowser__Korea:Ga0059261_1693 204 IVGTGSS--DPLTVAEADAMIFGYVLLNDWSARDIQAWEYQPLGPFQGKATATTISPWIVTAAALEPFR 270
                                               ****985..9*********************************************************** PP

                                 TIGR01266 275 vaqlePeqdpkplpylredradtafdielevslkteGlaeaavisrsnakslywtlkqqlahhsvnGcn 343
                                                +   P +++ +lpyl e   ++ +di+lev l++eG + ++visr+  +++y++ +qqlahhs +Gc+
  lcl|FitnessBrowser__Korea:Ga0059261_1693 271 AH--GPAREKPLLPYLDEP-GPMLYDIDLEVGLTPEG-GAESVISRTSYREMYYSAAQQLAHHSTAGCR 335
                                               *9..9***********999.9****************.8889*************************** PP

                                 TIGR01266 344 lraGdllgsGtisGkeeeafGsllelsakGkkevkladgetrkfledGdevilrgvckkeGvrvGfGec 412
                                               ++ Gdllg+GtisG+++++fGsllels++Gk+++ la g +r f+edGd++ilrg+c+ +G+r+GfG+c
  lcl|FitnessBrowser__Korea:Ga0059261_1693 336 MEVGDLLGTGTISGPDKGSFGSLLELSWGGKEPLTLAGGAQRSFVEDGDTLILRGQCRGDGYRIGFGDC 404
                                               ********************************************************************* PP

                                 TIGR01266 413 aGkvlpa 419
                                                G+v+pa
  lcl|FitnessBrowser__Korea:Ga0059261_1693 405 SGTVIPA 411
                                               *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (419 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.68
//
[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