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.3922165.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.11
//
[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:

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:

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:

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:

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