Alignments for a candidate for hmgA in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Mesorhizobium ciceri WSM1271

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate YP_004143708.1 Mesci_4549 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>NCBI__GCF_000185905.1:YP_004143708.1
          Length = 437

 Score =  721 bits (1862), Expect = 0.0
 Identities = 328/433 (75%), Positives = 379/433 (87%), Gaps = 2/433 (0%)

Query: 18  AAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRI 77
           A  YMPGFGNDFETE+LPG+LPQG+NSPQ+  YGLYAEQLSGSPFTAPRGTNERSWLYRI
Sbjct: 2   AFSYMPGFGNDFETETLPGSLPQGRNSPQRPAYGLYAEQLSGSPFTAPRGTNERSWLYRI 61

Query: 78  RPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTMTTAGD 137
           RPSV+HTGRF+   YP WK+AP+VG+H LALGQ RW+P+P P E  DF+ G+R++TTAGD
Sbjct: 62  RPSVKHTGRFKAASYPLWKSAPNVGDHELALGQYRWNPVPMPKEPTDFIAGMRSITTAGD 121

Query: 138 ALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEICLIPR 197
            L Q GMAAH Y  N  M DD+FFNADGELL+VP+ GA++  TE+G +++ P EI ++PR
Sbjct: 122 VLGQTGMAAHVYVANTSMADDHFFNADGELLVVPQVGALRFVTEMGVIELRPGEIAVLPR 181

Query: 198 GMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYEDKETPC 257
           G++FKV  +  E   RGY+CENYGAK TLPDRGPIGANCLANPRDFKTP A +E+KETPC
Sbjct: 182 GLVFKVELVDAEV--RGYVCENYGAKLTLPDRGPIGANCLANPRDFKTPCAWFEEKETPC 239

Query: 258 RVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLTA 317
           R+ VKWCG+FH+ EIGHSPLDVVAWHGNYAPYKYDL TFSPVGA+LFDHPDPSIFTVLTA
Sbjct: 240 RLIVKWCGNFHVTEIGHSPLDVVAWHGNYAPYKYDLATFSPVGALLFDHPDPSIFTVLTA 299

Query: 318 PSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFVPGGMS 377
           PSGEEGTAN+DFVIFPPRWLVAE TFRPPWYHRNIMSEFMGLI+G+YDAKE+GFVPGG+S
Sbjct: 300 PSGEEGTANIDFVIFPPRWLVAEDTFRPPWYHRNIMSEFMGLIHGQYDAKEQGFVPGGIS 359

Query: 378 LHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQDDYMD 437
           LHN+MLAHGPD  GFEKAS  ELKPVKLDNTMAFMFETRFPQ LT + AEL+T QD+Y+D
Sbjct: 360 LHNLMLAHGPDAPGFEKASRAELKPVKLDNTMAFMFETRFPQMLTRYGAELETRQDNYID 419

Query: 438 CWSGLERKFDGTP 450
           CW+ L+++F+GTP
Sbjct: 420 CWADLKKRFNGTP 432


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: 826
Number of extensions: 24
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: 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 YP_004143708.1 Mesci_4549 (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.10514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-211  688.4   0.0   1.9e-211  688.2   0.0    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004143708.1  Mesci_4549 homogentisate 1,2-dio


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004143708.1  Mesci_4549 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.2   0.0  1.9e-211  1.9e-211       2     429 .]       3     428 ..       2     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 688.2 bits;  conditional E-value: 1.9e-211
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               ++y++Gfgn+fe+e++pg+lP+G+nsPq+ +yglyaeqlsGs+ftaPr +n+rswlyrirPs++h++++
  lcl|NCBI__GCF_000185905.1:YP_004143708.1   3 FSYMPGFGNDFETETLPGSLPQGRNSPQRPAYGLYAEQLSGSPFTAPRGTNERSWLYRIRPSVKHTGRF 71 
                                               57******************************************************************* PP

                                 TIGR01015  71 elkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasm 138
                                               + +++  +++a+  + ++ +++q+rw+p+++p+ e +df+ g++++++agd+  ++G+a+h+y +n+sm
  lcl|NCBI__GCF_000185905.1:YP_004143708.1  72 KAASYPLWKSAPNVGDHElALGQYRWNPVPMPK-EPTDFIAGMRSITTAGDVLGQTGMAAHVYVANTSM 139
                                               ********999888877779************5.9********************************** PP

                                 TIGR01015 139 edevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfql 206
                                                d+ f+nadG+ll+vpq Gal+ +te+G+++++P+eiav+prG+ f+ve+   e+rGy++e+ygak +l
  lcl|NCBI__GCF_000185905.1:YP_004143708.1 140 ADDHFFNADGELLVVPQVGALRFVTEMGVIELRPGEIAVLPRGLVFKVELVdAEVRGYVCENYGAKLTL 208
                                               *************************************************98789*************** PP

                                 TIGR01015 207 PdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydl 275
                                               Pd+GPiGan+lanprdf++P a+fe+ke+  ++r+i k++g++++++++hspldvvawhGny+Pykydl
  lcl|NCBI__GCF_000185905.1:YP_004143708.1 209 PDRGPIGANCLANPRDFKTPCAWFEEKET--PCRLIVKWCGNFHVTEIGHSPLDVVAWHGNYAPYKYDL 275
                                               *****************************..9************************************* PP

                                 TIGR01015 276 kkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikG 344
                                                +f+ ++++ fdhpdPsiftvltaps +eGta++dfvifpPrwlvae+tfrPP+yhrn+msefmGli+G
  lcl|NCBI__GCF_000185905.1:YP_004143708.1 276 ATFSPVGALLFDHPDPSIFTVLTAPSGEEGTANIDFVIFPPRWLVAEDTFRPPWYHRNIMSEFMGLIHG 344
                                               ********************************************************************* PP

                                 TIGR01015 345 kydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelek 413
                                               +ydake+GfvpgG slhn+m ahGPd+ +fekas+aelkP k+d+ t+afmfe+++++ +t++++ele+
  lcl|NCBI__GCF_000185905.1:YP_004143708.1 345 QYDAKEQGFVPGGISLHNLMLAHGPDAPGFEKASRAELKPVKLDN-TMAFMFETRFPQMLTRYGAELET 412
                                               *********************************************.*********************** PP

                                 TIGR01015 414 ldedyeevwqglkkkf 429
                                                +++y ++w  lkk+f
  lcl|NCBI__GCF_000185905.1:YP_004143708.1 413 RQDNYIDCWADLKKRF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.94
//
[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