Alignments for a candidate for hmgA in Rhizobium etli CFN 42

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Rhizobium etli CFN 42

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate WP_011425039.1 RHE_RS08935 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>NCBI__GCF_000092045.1:WP_011425039.1
          Length = 453

 Score =  790 bits (2039), Expect = 0.0
 Identities = 367/433 (84%), Positives = 393/433 (90%)

Query: 21  YMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPS 80
           YMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPS
Sbjct: 21  YMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPS 80

Query: 81  VRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPSEALDFLQGIRTMTTAGDALT 140
           VRHT RF    YP WKTAP + EHSL LGQLRW P+PAP E L FLQG+RTMTTAGDA T
Sbjct: 81  VRHTRRFSNASYPLWKTAPCLDEHSLPLGQLRWDPIPAPEEKLTFLQGVRTMTTAGDAAT 140

Query: 141 QAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFTELGRMDVEPSEICLIPRGMM 200
           Q GM+AHAY FN DMVDDYFF+ADGELLIVP+ GAI+VFTE+G MDVEP EICL+PRGMM
Sbjct: 141 QVGMSAHAYVFNEDMVDDYFFDADGELLIVPQLGAIRVFTEMGIMDVEPLEICLVPRGMM 200

Query: 201 FKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAYEDKETPCRVQ 260
           FKV   GE+   RGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAA+EDKE PCRV 
Sbjct: 201 FKVMTTGEQTASRGYICENYGAKFTLPDRGPIGANCLANPRDFKTPVAAFEDKEKPCRVH 260

Query: 261 VKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLTAPSG 320
           VKWCG F++ EIGHSPLDVVAWHGNYAPYKYDL+TFSPVGAI FDHPDPSIF+VLTAP+ 
Sbjct: 261 VKWCGKFYVTEIGHSPLDVVAWHGNYAPYKYDLRTFSPVGAISFDHPDPSIFSVLTAPTE 320

Query: 321 EEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFVPGGMSLHN 380
           + GTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI+G+YDAKEEGFVPGG+SLHN
Sbjct: 321 DAGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIHGQYDAKEEGFVPGGISLHN 380

Query: 381 MMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQLTTFAAELDTLQDDYMDCWS 440
           MML HGPD   FEKASN ELKPVKLD+TMAFMFETR+PQQLT +AAEL+TLQDDY++CW 
Sbjct: 381 MMLPHGPDALAFEKASNVELKPVKLDHTMAFMFETRYPQQLTKYAAELETLQDDYLECWD 440

Query: 441 GLERKFDGTPGIK 453
           GLERKFDGTPGIK
Sbjct: 441 GLERKFDGTPGIK 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: 844
Number of extensions: 23
Number of successful extensions: 1
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_011425039.1 RHE_RS08935 (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.27100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-220  716.9   0.0   4.4e-220  716.7   0.0    1.0  1  lcl|NCBI__GCF_000092045.1:WP_011425039.1  RHE_RS08935 homogentisate 1,2-di


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092045.1:WP_011425039.1  RHE_RS08935 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.7   0.0  4.4e-220  4.4e-220       2     429 .]      19     446 ..      18     446 .. 0.98

  Alignments for each domain:
  == domain 1  score: 716.7 bits;  conditional E-value: 4.4e-220
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               lky++Gfgn+fe+e++pgalP+GqnsPqk++yglyaeqlsGs+ftaPr +n+rswlyrirPs++h+ ++
  lcl|NCBI__GCF_000092045.1:WP_011425039.1  19 LKYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPSVRHTRRF 87 
                                               79******************************************************************* PP

                                 TIGR01015  71 elkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasm 138
                                               + +++  ++ta+  +e+s  ++qlrw+p+++p+ e+++f++g++t+++agda+++ G+++h+y +n++m
  lcl|NCBI__GCF_000092045.1:WP_011425039.1  88 SNASYPLWKTAPCLDEHSlPLGQLRWDPIPAPE-EKLTFLQGVRTMTTAGDAATQVGMSAHAYVFNEDM 155
                                               ************9988885789**********5.9********************************** PP

                                 TIGR01015 139 edevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee...arGyilevygakf 204
                                                d++f++adG+llivpq Ga++++te+G ++veP ei+++prG++f+v  ++e   +rGyi+e+ygakf
  lcl|NCBI__GCF_000092045.1:WP_011425039.1 156 VDDYFFDADGELLIVPQLGAIRVFTEMGIMDVEPLEICLVPRGMMFKVMTTGEqtaSRGYICENYGAKF 224
                                               ************************************************999554669************ PP

                                 TIGR01015 205 qlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPyky 273
                                               +lPd+GPiGan+lanprdf++Pvaafedke   ++rv  k++gk+++++++hspldvvawhGny+Pyky
  lcl|NCBI__GCF_000092045.1:WP_011425039.1 225 TLPDRGPIGANCLANPRDFKTPVAAFEDKEK--PCRVHVKWCGKFYVTEIGHSPLDVVAWHGNYAPYKY 291
                                               ******************************9..99********************************** PP

                                 TIGR01015 274 dlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGli 342
                                               dl++f+ ++++sfdhpdPsif+vltap++ +Gta++dfvifpPrwlvae+tfrPP+yhrn+msefmGli
  lcl|NCBI__GCF_000092045.1:WP_011425039.1 292 DLRTFSPVGAISFDHPDPSIFSVLTAPTEDAGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 360
                                               ********************************************************************* PP

                                 TIGR01015 343 kGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakel 411
                                               +G+ydakeeGfvpgG slhn+m +hGPd+ afekasn+elkP k+d+ t+afmfe+++++++tk+a+el
  lcl|NCBI__GCF_000092045.1:WP_011425039.1 361 HGQYDAKEEGFVPGGISLHNMMLPHGPDALAFEKASNVELKPVKLDH-TMAFMFETRYPQQLTKYAAEL 428
                                               **********************************************9.********************* PP

                                 TIGR01015 412 ekldedyeevwqglkkkf 429
                                               e+l++dy e+w+gl++kf
  lcl|NCBI__GCF_000092045.1:WP_011425039.1 429 ETLQDDYLECWDGLERKF 446
                                               ****************98 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: 00:00:00.01
# Mc/sec: 12.67
//
[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