Alignments for a candidate for hmgA in Methylocystis bryophila S285

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Methylocystis bryophila S285

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate WP_085772521.1 B1812_RS16265 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>NCBI__GCF_002117405.1:WP_085772521.1
          Length = 437

 Score =  573 bits (1477), Expect = e-168
 Identities = 271/432 (62%), Positives = 323/432 (74%), Gaps = 4/432 (0%)

Query: 18  AAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRI 77
           A  YM GFGN+FETE+L GALP+GQN+PQ+C YGL+AEQ+SG+ FTAP G N RSWLYR+
Sbjct: 4   ALAYMAGFGNEFETEALAGALPKGQNAPQRCPYGLFAEQISGTAFTAPHGLNRRSWLYRL 63

Query: 78  RPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTMTTAGD 137
           RPSV H  RF + D P WKTAP     + ++G  RWSP P P+E L F+ G+RT+TTAG 
Sbjct: 64  RPSVLHARRFAKRDQPLWKTAP-ASSPAQSVGAFRWSPSPMPTEELSFIAGVRTITTAGS 122

Query: 138 ALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEICLIPR 197
           A  + GMAAH Y     M D YF NADGELLI P+ G + +FTE GR+   P EIC+IPR
Sbjct: 123 ADLRIGMAAHLYFVTQSMHDTYFCNADGELLIAPQQGELDLFTEFGRLHAAPGEICVIPR 182

Query: 198 GMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYEDKETPC 257
           G+ FKVT  G     RGY+CENYGA F LP+RG IGAN LAN RDF  PVAA+ED+E P 
Sbjct: 183 GVKFKVTVAGPA---RGYLCENYGAPFALPNRGAIGANGLANARDFHAPVAAFEDREEPG 239

Query: 258 RVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLTA 317
            +  KW G F    +G+SPLDVVAWHG+YAPYKYDL+ F P+GA+LFDHPDPSI TVL++
Sbjct: 240 VLTFKWGGDFFDCALGYSPLDVVAWHGSYAPYKYDLRLFCPMGALLFDHPDPSINTVLSS 299

Query: 318 PSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFVPGGMS 377
            S E G ANVDFVIFP RW VAEH+FRPPW+H N+MSEFMGLI+GRYDAK EGF PGG+S
Sbjct: 300 ASAETGVANVDFVIFPDRWQVAEHSFRPPWHHVNVMSEFMGLIFGRYDAKPEGFEPGGVS 359

Query: 378 LHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQDDYMD 437
           LHN +  HGPD + +E A   ELKP ++   +AFMFETRFPQ LT +AA L TLQ DY D
Sbjct: 360 LHNALCPHGPDATAYELARASELKPERMSGALAFMFETRFPQHLTDYAATLPTLQKDYAD 419

Query: 438 CWSGLERKFDGT 449
           CWSGL ++FDG+
Sbjct: 420 CWSGLRKRFDGS 431


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: 762
Number of extensions: 31
Number of successful extensions: 3
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: 437
Length adjustment: 32
Effective length of query: 421
Effective length of database: 405
Effective search space:   170505
Effective search space used:   170505
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_085772521.1 B1812_RS16265 (homogentisate 1,2-dioxygenase)
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.8820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-193  629.8   0.0   1.1e-193  629.7   0.0    1.0  1  lcl|NCBI__GCF_002117405.1:WP_085772521.1  B1812_RS16265 homogentisate 1,2-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085772521.1  B1812_RS16265 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.7   0.0  1.1e-193  1.1e-193       2     429 .]       5     428 ..       4     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 629.7 bits;  conditional E-value: 1.1e-193
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               l+y++Gfgnefe+ea++galP+Gqn+Pq++pygl+aeq+sG+aftaP   n+rswlyr+rPs+ h  ++
  lcl|NCBI__GCF_002117405.1:WP_085772521.1   5 LAYMAGFGNEFETEALAGALPKGQNAPQRCPYGLFAEQISGTAFTAPHGLNRRSWLYRLRPSVLHARRF 73 
                                               78******************************************************************* PP

                                 TIGR01015  71 elkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasme 139
                                               +++++  ++ta++++ a++ + +rwsp ++p+ e++ f+ g++t+++ag a  r G+a+hly v++sm+
  lcl|NCBI__GCF_002117405.1:WP_085772521.1  74 AKRDQPLWKTAPASSPAQSVGAFRWSPSPMPT-EELSFIAGVRTITTAGSADLRIGMAAHLYFVTQSMH 141
                                               *******************************7.99********************************** PP

                                 TIGR01015 140 devfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveeearGyilevygakfqlPd 208
                                               d++f nadG+lli pq+G+l+++te+Grl+++P+ei+viprGv+f+v+v ++arGy++e+yga f lP+
  lcl|NCBI__GCF_002117405.1:WP_085772521.1 142 DTYFCNADGELLIAPQQGELDLFTEFGRLHAAPGEICVIPRGVKFKVTVAGPARGYLCENYGAPFALPN 210
                                               ********************************************************************* PP

                                 TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277
                                               +G iGanglan+rdf+aPvaafed+e   +  ++ k+ g++f +  ++spldvvawhG y+Pykydl+ 
  lcl|NCBI__GCF_002117405.1:WP_085772521.1 211 RGAIGANGLANARDFHAPVAAFEDREE--PGVLTFKWGGDFFDCALGYSPLDVVAWHGSYAPYKYDLRL 277
                                               **************************9..568899********************************** PP

                                 TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346
                                               f  ++++ fdhpdPsi tvl++ s ++G+a++dfvifp rw+vae++frPP++h nvmsefmGli G+y
  lcl|NCBI__GCF_002117405.1:WP_085772521.1 278 FCPMGALLFDHPDPSINTVLSSASAETGVANVDFVIFPDRWQVAEHSFRPPWHHVNVMSEFMGLIFGRY 346
                                               ********************************************************************* PP

                                 TIGR01015 347 dakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelekld 415
                                               dak eGf pgG slhn++ +hGPd++a+e a ++elkPe+++  +lafmfe+++++++t++a++l +l+
  lcl|NCBI__GCF_002117405.1:WP_085772521.1 347 DAKPEGFEPGGVSLHNALCPHGPDATAYELARASELKPERMSG-ALAFMFETRFPQHLTDYAATLPTLQ 414
                                               *****************************************87.************************* PP

                                 TIGR01015 416 edyeevwqglkkkf 429
                                               +dy ++w+gl+k+f
  lcl|NCBI__GCF_002117405.1:WP_085772521.1 415 KDYADCWSGLRKRF 428
                                               ***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (437 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: 8.17
//
[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