Alignments for a candidate for hmgA in Methylobacterium sp. 4-46

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Methylobacterium sp. 4-46

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate WP_012332381.1 M446_RS12065 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>NCBI__GCF_000019365.1:WP_012332381.1
          Length = 453

 Score =  568 bits (1464), Expect = e-166
 Identities = 282/429 (65%), Positives = 321/429 (74%), Gaps = 4/429 (0%)

Query: 20  GYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRP 79
           GYM GFGN FETE+LPGALP G+NSPQ C YGLYAEQLSGSPFTAPR  NERSWLYRIRP
Sbjct: 21  GYMSGFGNGFETEALPGALPIGRNSPQICPYGLYAEQLSGSPFTAPRTANERSWLYRIRP 80

Query: 80  SVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTMTTAGDAL 139
           +V H G FR+VD   W TAP      L    LRW P+  PSE L F++GI T+TTAGDA 
Sbjct: 81  TVMHWGDFRKVDARLWLTAP-AELVDLPPAPLRWDPVAIPSEPLSFVEGICTVTTAGDAG 139

Query: 140 TQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEICLIPRGM 199
            QAGM AH Y     M D+YF NADGE+L+VP+ GA++  TE G +DVEP E+C+IPRG+
Sbjct: 140 AQAGMGAHFYFATRSMPDEYFSNADGEMLVVPQEGALRWRTEFGIIDVEPGEVCVIPRGV 199

Query: 200 MFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYEDKETPCRV 259
              V  LG     RGY+CENYG  FTLP+RGPIGANCLAN RDF TPVAAYED++ P  +
Sbjct: 200 KVAVDLLGGPA--RGYVCENYGGAFTLPERGPIGANCLANQRDFLTPVAAYEDRDAPGTM 257

Query: 260 QVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLTAPS 319
            VKW G+    EI HSPLDVVAWHGNYAPYKYDL+ FSPVG ILFDH DPSIFTVLT+PS
Sbjct: 258 LVKWGGALWAAEIDHSPLDVVAWHGNYAPYKYDLRKFSPVGPILFDHADPSIFTVLTSPS 317

Query: 320 GEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKE-EGFVPGGMSL 378
              GTAN+DFVIF  RWLVAE+TFRPPWYH N+MSEFMGL+YG YDAK   GF PGG SL
Sbjct: 318 ETPGTANIDFVIFSDRWLVAENTFRPPWYHLNVMSEFMGLVYGVYDAKTGGGFRPGGASL 377

Query: 379 HNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQDDYMDC 438
           HN +L HGPD   FE+ASN +LKP KL+ T+AFMFETRFPQ+++ FAAE    Q DY   
Sbjct: 378 HNTLLPHGPDVDAFERASNVDLKPHKLEGTLAFMFETRFPQKVSRFAAETPARQKDYAAY 437

Query: 439 WSGLERKFD 447
              L + FD
Sbjct: 438 GRKLAKHFD 446


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: 818
Number of extensions: 35
Number of successful extensions: 4
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 WP_012332381.1 M446_RS12065 (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.29736.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   0.0   1.7e-199  648.8   0.0    1.0  1  lcl|NCBI__GCF_000019365.1:WP_012332381.1  M446_RS12065 homogentisate 1,2-d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012332381.1  M446_RS12065 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.8   0.0  1.7e-199  1.7e-199       3     429 .]      21     445 ..      19     445 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.8 bits;  conditional E-value: 1.7e-199
                                 TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 
                                                y+sGfgn fe+ea+pgalP G+nsPq +pyglyaeqlsGs+ftaPr+ n+rswlyrirP+++h + ++
  lcl|NCBI__GCF_000019365.1:WP_012332381.1  21 GYMSGFGNGFETEALPGALPIGRNSPQICPYGLYAEQLSGSPFTAPRTANERSWLYRIRPTVMHWGDFR 89 
                                               5******************************************************************** PP

                                 TIGR01015  72 lkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmed 140
                                               + +   +lta+++ ++  p  lrw+p+ ips e + fveg+ t+++agda ++aG+++h y ++ sm d
  lcl|NCBI__GCF_000019365.1:WP_012332381.1  90 KVDARLWLTAPAELVDLPPAPLRWDPVAIPS-EPLSFVEGICTVTTAGDAGAQAGMGAHFYFATRSMPD 157
                                               **************999*************8.9************************************ PP

                                 TIGR01015 141 evfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPd 208
                                               e+f+nadG++l+vpq+Gal+ +te+G ++veP+e++viprGv+ +v++  ++arGy++e+yg +f+lP+
  lcl|NCBI__GCF_000019365.1:WP_012332381.1 158 EYFSNADGEMLVVPQEGALRWRTEFGIIDVEPGEVCVIPRGVKVAVDLLgGPARGYVCENYGGAFTLPE 226
                                               ************************************************9999***************** PP

                                 TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277
                                               +GPiGan+lan rdf +Pvaa+ed+++  + +++ k+ g+l+aa++dhspldvvawhGny+Pykydl+k
  lcl|NCBI__GCF_000019365.1:WP_012332381.1 227 RGPIGANCLANQRDFLTPVAAYEDRDA--PGTMLVKWGGALWAAEIDHSPLDVVAWHGNYAPYKYDLRK 293
                                               ***************************..669999********************************** PP

                                 TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346
                                               f+ ++ + fdh+dPsiftvlt+ps+++Gta++dfvif+ rwlvae+tfrPP+yh nvmsefmGl++G y
  lcl|NCBI__GCF_000019365.1:WP_012332381.1 294 FSPVGPILFDHADPSIFTVLTSPSETPGTANIDFVIFSDRWLVAENTFRPPWYHLNVMSEFMGLVYGVY 362
                                               ********************************************************************* PP

                                 TIGR01015 347 dakeeG.fvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelekl 414
                                               dak++G f pgGaslhn + +hGPdv+afe+asn++lkP+k++  tlafmfe++++++v+++a+e+ + 
  lcl|NCBI__GCF_000019365.1:WP_012332381.1 363 DAKTGGgFRPGGASLHNTLLPHGPDVDAFERASNVDLKPHKLEG-TLAFMFETRFPQKVSRFAAETPAR 430
                                               ***9877***********************************76.************************ PP

                                 TIGR01015 415 dedyeevwqglkkkf 429
                                               ++dy +  + l k+f
  lcl|NCBI__GCF_000019365.1:WP_012332381.1 431 QKDYAAYGRKLAKHF 445
                                               ******999999997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.96
//
[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