Alignments for a candidate for hmgA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Phaeobacter inhibens BS107

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate GFF44 PGA1_c00440 homogentisate 1,2-dioxygenase HmgA

Query= SwissProt::Q9X4F5
         (453 letters)



>FitnessBrowser__Phaeo:GFF44
          Length = 453

 Score =  650 bits (1676), Expect = 0.0
 Identities = 296/434 (68%), Positives = 353/434 (81%), Gaps = 2/434 (0%)

Query: 20  GYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRP 79
           GYMPGFGNDFETE+LPGALPQG NSPQKCNYGLY EQLSG+ FTAP   NER+W YRIRP
Sbjct: 22  GYMPGFGNDFETEALPGALPQGMNSPQKCNYGLYGEQLSGTAFTAPSHQNERTWCYRIRP 81

Query: 80  SVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTMTTAGDAL 139
           SV+H+ R+ ++D P+WK+AP+V    ++LGQ RW P+P  +E L +L G+RTMTTAGD  
Sbjct: 82  SVKHSHRYTKIDLPYWKSAPNVDPDVISLGQYRWDPVPHGTEGLTWLTGMRTMTTAGDVN 141

Query: 140 TQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEICLIPRGM 199
           TQ GMA+H Y     M+D YF++AD ELL+VP+ G ++  TELG +D+EP EI +IPRG+
Sbjct: 142 TQVGMASHIYLVTDSMMDSYFYSADSELLVVPQEGRLRFATELGIIDIEPQEIAIIPRGL 201

Query: 200 MFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYEDKETPCRV 259
           +++V  L  +   RG++CENYG KF LP RGPIGANC+ANPRDFK PVAA+ED+ETP  V
Sbjct: 202 VYRVEVL--DGPCRGFVCENYGQKFELPGRGPIGANCMANPRDFKAPVAAFEDRETPSTV 259

Query: 260 QVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLTAPS 319
            +KWCG FH  +IGHSPLDVVAWHGNY P KYDL+T+ PVGAILFDHPDPSIFTVLTAPS
Sbjct: 260 TIKWCGQFHETKIGHSPLDVVAWHGNYTPVKYDLRTYCPVGAILFDHPDPSIFTVLTAPS 319

Query: 320 GEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFVPGGMSLH 379
           G+ GTAN+DFV+F  RW+VAE TFRPPWYH+NIMSE MG IYG+YDAK +GFVPGG+SLH
Sbjct: 320 GQPGTANIDFVLFRERWMVAEDTFRPPWYHKNIMSELMGNIYGQYDAKPQGFVPGGVSLH 379

Query: 380 NMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQDDYMDCW 439
           NMML HGPD + FE ASN +L P KLDNTM+FMFETRFPQ LT FAA    LQDDY+DCW
Sbjct: 380 NMMLPHGPDRNAFEGASNADLGPEKLDNTMSFMFETRFPQHLTPFAANEAPLQDDYIDCW 439

Query: 440 SGLERKFDGTPGIK 453
           + +E+KFDGTPG K
Sbjct: 440 ADIEKKFDGTPGKK 453


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: 820
Number of extensions: 35
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: 453
Length adjustment: 33
Effective length of query: 420
Effective length of database: 420
Effective search space:   176400
Effective search space used:   176400
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 GFF44 PGA1_c00440 (homogentisate 1,2-dioxygenase HmgA)
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.1314.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.5e-199  649.0   0.1   1.7e-199  648.8   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF44  PGA1_c00440 homogentisate 1,2-di


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF44  PGA1_c00440 homogentisate 1,2-dioxygenase HmgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.8   0.1  1.7e-199  1.7e-199       3     429 .]      22     446 ..      20     446 .. 0.98

  Alignments for each domain:
  == domain 1  score: 648.8 bits;  conditional E-value: 1.7e-199
                        TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkeseeklt 80 
                                       y++Gfgn+fe+ea+pgalP+G nsPqk++ygly eqlsG+aftaP ++n+r+w yrirPs++h+ + ++ +  ++++
  lcl|FitnessBrowser__Phaeo:GFF44  22 GYMPGFGNDFETEALPGALPQGMNSPQKCNYGLYGEQLSGTAFTAPSHQNERTWCYRIRPSVKHSHRYTKIDLPYWKS 99 
                                      6******************************************************************99999****99 PP

                        TIGR01015  81 anfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdllivpqkG 157
                                      a+  + ++ +++q+rw+p++  + e ++++ g++t+++agd++++ G+a h+y+v+ sm d++fy+ad +ll+vpq+G
  lcl|FitnessBrowser__Phaeo:GFF44 100 APNVDPDViSLGQYRWDPVPHGT-EGLTWLTGMRTMTTAGDVNTQVGMASHIYLVTDSMMDSYFYSADSELLVVPQEG 176
                                      99888887799*********975.9***************************************************** PP

                        TIGR01015 158 aleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlGPiGanglanprdfeaPvaafedke 234
                                       l+  telG +++eP+eia+iprG+ +rvev  ++ rG+++e+yg+kf+lP +GPiGan++anprdf+aPvaafed+e
  lcl|FitnessBrowser__Phaeo:GFF44 177 RLRFATELGIIDIEPQEIAIIPRGLVYRVEVLdGPCRGFVCENYGQKFELPGRGPIGANCMANPRDFKAPVAAFEDRE 254
                                      *******************************989******************************************** PP

                        TIGR01015 235 vkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfv 312
                                      +  + +v+ k++g+++ +k++hspldvvawhGny+P kydl+++  ++++ fdhpdPsiftvltaps ++Gta++dfv
  lcl|FitnessBrowser__Phaeo:GFF44 255 T--PSTVTIKWCGQFHETKIGHSPLDVVAWHGNYTPVKYDLRTYCPVGAILFDHPDPSIFTVLTAPSGQPGTANIDFV 330
                                      *..779999********************************************************************* PP

                        TIGR01015 313 ifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddg 390
                                      +f  rw+vae+tfrPP+yh+n+mse mG i+G+ydak +GfvpgG slhn+m +hGPd +afe asna+l Pek+d+ 
  lcl|FitnessBrowser__Phaeo:GFF44 331 LFRERWMVAEDTFRPPWYHKNIMSELMGNIYGQYDAKPQGFVPGGVSLHNMMLPHGPDRNAFEGASNADLGPEKLDN- 407
                                      *****************************************************************************. PP

                        TIGR01015 391 tlafmfesslslavtklakelekldedyeevwqglkkkf 429
                                      t++fmfe+++++++t +a++ + l++dy ++w  ++kkf
  lcl|FitnessBrowser__Phaeo:GFF44 408 TMSFMFETRFPQHLTPFAANEAPLQDDYIDCWADIEKKF 446
                                      ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (453 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: 00:00:00.02
# Mc/sec: 7.91
//
[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