Alignments for a candidate for hmgA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Sphingomonas koreensis DSMZ 15582

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate Ga0059261_1694 Ga0059261_1694 homogentisate 1,2-dioxygenase (EC 1.13.11.5)

Query= SwissProt::Q9X4F5
         (453 letters)



>FitnessBrowser__Korea:Ga0059261_1694
          Length = 441

 Score =  644 bits (1660), Expect = 0.0
 Identities = 296/437 (67%), Positives = 349/437 (79%), Gaps = 2/437 (0%)

Query: 13  SGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERS 72
           S   +A GYMPGFGNDFETE+LPGALPQGQNSPQKC YGLYAEQLSG+ FTAPRG NERS
Sbjct: 3   SHNMQAVGYMPGFGNDFETEALPGALPQGQNSPQKCPYGLYAEQLSGTAFTAPRGQNERS 62

Query: 73  WLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTM 132
           W YRIRPSVRH GRF  ++ PHWK+AP++     +LGQ RW+P+P  +  L +L G+RT+
Sbjct: 63  WCYRIRPSVRHVGRFAAIELPHWKSAPNIVPGVASLGQYRWNPVPHGAGELTWLTGMRTV 122

Query: 133 TTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEI 192
           TTAGD  TQ GMA+H Y   A MVD YF++ADGELL+VP+ G ++  TELG +++ P EI
Sbjct: 123 TTAGDVNTQTGMASHVYLVTASMVDSYFYSADGELLVVPQEGRLRFCTELGVIEIAPGEI 182

Query: 193 CLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYED 252
            ++PRG++++V  +  +   RG++CENYG  F LPDRGPIGANC+ANPRDFKTPVAA+ED
Sbjct: 183 AVLPRGLVYRVEVI--DGPCRGFVCENYGQPFALPDRGPIGANCMANPRDFKTPVAAFED 240

Query: 253 KETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIF 312
           +ETP  + +KWCG FH   I HSPLDVVAWHGNYAPYKYDL T+SPVGAILFDHPDPSIF
Sbjct: 241 RETPSTLTIKWCGQFHQSAIPHSPLDVVAWHGNYAPYKYDLSTYSPVGAILFDHPDPSIF 300

Query: 313 TVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFV 372
           TVLTA S   GTAN+DFV+F  RWLVAEH+FRPPWYH+N+MSE MG IYG YDAK +GF 
Sbjct: 301 TVLTARSEIPGTANIDFVLFRERWLVAEHSFRPPWYHKNVMSELMGNIYGEYDAKPDGFA 360

Query: 373 PGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQ 432
           PGGMSLHN ML HGPD + FEKASN  LKP KLD TM+FMFETRFPQ LT +AA    LQ
Sbjct: 361 PGGMSLHNCMLPHGPDRNAFEKASNAALKPEKLDKTMSFMFETRFPQHLTDWAAREAPLQ 420

Query: 433 DDYMDCWSGLERKFDGT 449
            DY DCW GL++KFDG+
Sbjct: 421 SDYADCWDGLDKKFDGS 437


Lambda     K      H
   0.320    0.138    0.442 

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: 829
Number of extensions: 37
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: 453
Length of database: 441
Length adjustment: 33
Effective length of query: 420
Effective length of database: 408
Effective search space:   171360
Effective search space used:   171360
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 Ga0059261_1694 Ga0059261_1694 (homogentisate 1,2-dioxygenase (EC 1.13.11.5))
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

# 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/TIGR01015.hmm
# target sequence database:        /tmp/gapView.25137.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01015  [M=429]
Accession:   TIGR01015
Description: hmgA: homogentisate 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-203  659.9   0.0   8.5e-203  659.7   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1694  Ga0059261_1694 homogentisate 1,2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1694  Ga0059261_1694 homogentisate 1,2-dioxygenase (EC 1.13.11.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  659.7   0.0  8.5e-203  8.5e-203       2     429 .]       9     434 ..       8     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 659.7 bits;  conditional E-value: 8.5e-203
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               + y++Gfgn+fe+ea+pgalP+GqnsPqk+pyglyaeqlsG+aftaPr +n+rsw yrirPs++h +++
  lcl|FitnessBrowser__Korea:Ga0059261_1694   9 VGYMPGFGNDFETEALPGALPQGQNSPQKCPYGLYAEQLSGTAFTAPRGQNERSWCYRIRPSVRHVGRF 77 
                                               57******************************************************************* PP

                                 TIGR01015  71 elkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasm 138
                                               +  e  ++++a+     + +++q+rw+p++   + +++++ g++t+++agd+++++G+a h+y+v+asm
  lcl|FitnessBrowser__Korea:Ga0059261_1694  78 AAIELPHWKSAPNIVPGVaSLGQYRWNPVPHG-AGELTWLTGMRTVTTAGDVNTQTGMASHVYLVTASM 145
                                               ***999999987665555489********996.589********************************* PP

                                 TIGR01015 139 edevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfql 206
                                                d++fy+adG+ll+vpq+G l+  telG+++++P+eiav+prG+ +rvev  ++ rG+++e+yg+ f l
  lcl|FitnessBrowser__Korea:Ga0059261_1694 146 VDSYFYSADGELLVVPQEGRLRFCTELGVIEIAPGEIAVLPRGLVYRVEVIdGPCRGFVCENYGQPFAL 214
                                               *************************************************9989**************** PP

                                 TIGR01015 207 PdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydl 275
                                               Pd+GPiGan++anprdf++Pvaafed+e+  + +++ k++g+++++ + hspldvvawhGny+Pykydl
  lcl|FitnessBrowser__Korea:Ga0059261_1694 215 PDRGPIGANCMANPRDFKTPVAAFEDRET--PSTLTIKWCGQFHQSAIPHSPLDVVAWHGNYAPYKYDL 281
                                               *****************************..779999******************************** PP

                                 TIGR01015 276 kkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikG 344
                                               ++++ ++++ fdhpdPsiftvlta+s+ +Gta++dfv+f  rwlvae++frPP+yh+nvmse mG i+G
  lcl|FitnessBrowser__Korea:Ga0059261_1694 282 STYSPVGAILFDHPDPSIFTVLTARSEIPGTANIDFVLFRERWLVAEHSFRPPWYHKNVMSELMGNIYG 350
                                               ********************************************************************* PP

                                 TIGR01015 345 kydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelek 413
                                               +ydak +Gf+pgG+slhn+m +hGPd +afekasna lkPek+d+ t++fmfe+++++++t++a++ + 
  lcl|FitnessBrowser__Korea:Ga0059261_1694 351 EYDAKPDGFAPGGMSLHNCMLPHGPDRNAFEKASNAALKPEKLDK-TMSFMFETRFPQHLTDWAAREAP 418
                                               ********************************************9.*********************** PP

                                 TIGR01015 414 ldedyeevwqglkkkf 429
                                               l++dy ++w+gl+kkf
  lcl|FitnessBrowser__Korea:Ga0059261_1694 419 LQSDYADCWDGLDKKF 434
                                               *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (441 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: 11.50
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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