Alignments for a candidate for hmgA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Dinoroseobacter shibae DFL-12

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate 3610431 Dshi_3812 homogentisate 1,2-dioxygenase (RefSeq)

Query= SwissProt::Q9X4F5
         (453 letters)



>FitnessBrowser__Dino:3610431
          Length = 451

 Score =  627 bits (1617), Expect = 0.0
 Identities = 293/444 (65%), Positives = 345/444 (77%), Gaps = 4/444 (0%)

Query: 10  RAGSGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTN 69
           RA +      GYMPGFGNDFETE+LPGALPQG NSPQKCNYGLY EQLSG+ FT  R   
Sbjct: 12  RAATPMGTTEGYMPGFGNDFETEALPGALPQGMNSPQKCNYGLYGEQLSGTAFTDVRP-- 69

Query: 70  ERSWLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGI 129
           ER+W YRIRPSV+H+ R+RRV+ P++++AP +     +LGQ RW P+P     L +L G+
Sbjct: 70  ERTWCYRIRPSVKHSHRYRRVELPYFRSAPDIHPEVTSLGQYRWDPVPHTDAPLTWLTGM 129

Query: 130 RTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEP 189
           RTMTTAGD  TQ GMAAH Y     M D YF++AD E+L+VP+ G ++  TELG +D+EP
Sbjct: 130 RTMTTAGDVNTQVGMAAHVYLVTESMQDAYFYSADSEMLVVPQEGRLRFATELGIIDLEP 189

Query: 190 SEICLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAA 249
            EI ++PRG++++V  L      RG++CENYG KF LP RGPIGANC+ANPRDFKTPVAA
Sbjct: 190 KEIAILPRGLLYRVELLDGPA--RGFVCENYGQKFELPGRGPIGANCMANPRDFKTPVAA 247

Query: 250 YEDKETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDP 309
           +ED+E P  V VKWCG FH  +IG SPLDVVAWHGNYAP KYDL+ + PVGAILFDHPDP
Sbjct: 248 FEDREVPSTVTVKWCGQFHETQIGQSPLDVVAWHGNYAPCKYDLRNYCPVGAILFDHPDP 307

Query: 310 SIFTVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEE 369
           SIFTVLTAPSG+ GTAN+DFV+F  RW+VAE TFRPPWYH+NIMSE MG IYG+YDAK +
Sbjct: 308 SIFTVLTAPSGQPGTANIDFVLFRERWMVAEDTFRPPWYHKNIMSELMGNIYGQYDAKPQ 367

Query: 370 GFVPGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELD 429
           GFVPGG+SLHNMML HGPD   FEKASN  L P KLDNTM+FMFETRFPQ LT FA    
Sbjct: 368 GFVPGGISLHNMMLPHGPDRDAFEKASNANLGPDKLDNTMSFMFETRFPQHLTRFAGTEA 427

Query: 430 TLQDDYMDCWSGLERKFDGTPGIK 453
            LQDDY+DCW  +E+KFDGTPG K
Sbjct: 428 PLQDDYIDCWKDIEKKFDGTPGKK 451


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: 803
Number of extensions: 30
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: 451
Length adjustment: 33
Effective length of query: 420
Effective length of database: 418
Effective search space:   175560
Effective search space used:   175560
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 3610431 Dshi_3812 (homogentisate 1,2-dioxygenase (RefSeq))
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.373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.9e-193  627.1   0.0   7.9e-193  626.9   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610431  Dshi_3812 homogentisate 1,2-diox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610431  Dshi_3812 homogentisate 1,2-dioxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  626.9   0.0  7.9e-193  7.9e-193       3     429 .]      22     444 ..      20     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 626.9 bits;  conditional E-value: 7.9e-193
                         TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkeseekl 79 
                                        y++Gfgn+fe+ea+pgalP+G nsPqk++ygly eqlsG+aft  r   +r+w yrirPs++h+ + ++ e  +++
  lcl|FitnessBrowser__Dino:3610431  22 GYMPGFGNDFETEALPGALPQGMNSPQKCNYGLYGEQLSGTAFTDVRP--ERTWCYRIRPSVKHSHRYRRVELPYFR 96 
                                       6********************************************997..69*******************999998 PP

                         TIGR01015  80 tanfke.easdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdllivpq 155
                                       +a+  + e ++++q+rw+p++   ++ ++++ g++t+++agd++++ G+a+h+y+v++sm+d +fy+ad ++l+vpq
  lcl|FitnessBrowser__Dino:3610431  97 SAPDIHpEVTSLGQYRWDPVPHT-DAPLTWLTGMRTMTTAGDVNTQVGMAAHVYLVTESMQDAYFYSADSEMLVVPQ 172
                                       88655405559**********96.69*************************************************** PP

                         TIGR01015 156 kGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlGPiGanglanprdfeaPvaafe 231
                                       +G l+  telG +++eP+eia++prG+ +rve+  ++arG+++e+yg+kf+lP +GPiGan++anprdf++Pvaafe
  lcl|FitnessBrowser__Dino:3610431 173 EGRLRFATELGIIDLEPKEIAILPRGLLYRVELLdGPARGFVCENYGQKFELPGRGPIGANCMANPRDFKTPVAAFE 249
                                       ********************************9989***************************************** PP

                         TIGR01015 232 dkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtai 308
                                       d+ev  + +v+ k++g+++ +++++spldvvawhGny+P kydl+++  ++++ fdhpdPsiftvltaps ++Gta+
  lcl|FitnessBrowser__Dino:3610431 250 DREV--PSTVTVKWCGQFHETQIGQSPLDVVAWHGNYAPCKYDLRNYCPVGAILFDHPDPSIFTVLTAPSGQPGTAN 324
                                       ****..7799******************************************************************* PP

                         TIGR01015 309 adfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPe 385
                                       +dfv+f  rw+vae+tfrPP+yh+n+mse mG i+G+ydak +GfvpgG slhn+m +hGPd +afekasna+l P+
  lcl|FitnessBrowser__Dino:3610431 325 IDFVLFRERWMVAEDTFRPPWYHKNIMSELMGNIYGQYDAKPQGFVPGGISLHNMMLPHGPDRDAFEKASNANLGPD 401
                                       ***************************************************************************** PP

                         TIGR01015 386 kiddgtlafmfesslslavtklakelekldedyeevwqglkkkf 429
                                       k+d+ t++fmfe+++++++t++a + + l++dy ++w+ ++kkf
  lcl|FitnessBrowser__Dino:3610431 402 KLDN-TMSFMFETRFPQHLTRFAGTEAPLQDDYIDCWKDIEKKF 444
                                       ****.************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (451 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: 9.47
//
[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:

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