Alignments for a candidate for hmgA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Sinorhizobium meliloti 1021

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate SMc03208 SMc03208 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>FitnessBrowser__Smeli:SMc03208
          Length = 453

 Score =  956 bits (2470), Expect = 0.0
 Identities = 453/453 (100%), Positives = 453/453 (100%)

Query: 1   MLEKAEKQRRAGSGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS 60
           MLEKAEKQRRAGSGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS
Sbjct: 1   MLEKAEKQRRAGSGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS 60

Query: 61  PFTAPRGTNERSWLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPS 120
           PFTAPRGTNERSWLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPS
Sbjct: 61  PFTAPRGTNERSWLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPS 120

Query: 121 EALDFLQGIRTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFT 180
           EALDFLQGIRTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFT
Sbjct: 121 EALDFLQGIRTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFT 180

Query: 181 ELGRMDVEPSEICLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANP 240
           ELGRMDVEPSEICLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANP
Sbjct: 181 ELGRMDVEPSEICLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANP 240

Query: 241 RDFKTPVAAYEDKETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG 300
           RDFKTPVAAYEDKETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG
Sbjct: 241 RDFKTPVAAYEDKETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG 300

Query: 301 AILFDHPDPSIFTVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 360
           AILFDHPDPSIFTVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI
Sbjct: 301 AILFDHPDPSIFTVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 360

Query: 361 YGRYDAKEEGFVPGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQ 420
           YGRYDAKEEGFVPGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQ
Sbjct: 361 YGRYDAKEEGFVPGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQ 420

Query: 421 LTTFAAELDTLQDDYMDCWSGLERKFDGTPGIK 453
           LTTFAAELDTLQDDYMDCWSGLERKFDGTPGIK
Sbjct: 421 LTTFAAELDTLQDDYMDCWSGLERKFDGTPGIK 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: 953
Number of extensions: 27
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 SMc03208 SMc03208 (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.22957.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     3e-230  750.2   0.1   3.4e-230  750.0   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc03208  SMc03208 homogentisate 1,2-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03208  SMc03208 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  750.0   0.1  3.4e-230  3.4e-230       3     429 .]      20     446 ..      18     446 .. 0.99

  Alignments for each domain:
  == domain 1  score: 750.0 bits;  conditional E-value: 3.4e-230
                           TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkesee 77 
                                          y++Gfgn+fe+e++pgalP+GqnsPqk++yglyaeqlsGs+ftaPr +n+rswlyrirPs++h++++++ ++ +
  lcl|FitnessBrowser__Smeli:SMc03208  20 GYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPSVRHTGRFRRVDYPH 94 
                                         7************************************************************************** PP

                           TIGR01015  78 kltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdll 151
                                         ++ta++ +e+s +++qlrwspl++ps ea+df++g++t+++agda ++aG+a+h+ya+na+m d++f+nadG+ll
  lcl|FitnessBrowser__Smeli:SMc03208  95 WKTAPHVGEHSlALGQLRWSPLPAPS-EALDFLQGIRTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELL 168
                                         *******999989************8.9*********************************************** PP

                           TIGR01015 152 ivpqkGaleittelGrlkvePneiaviprGvrfrveveee...arGyilevygakfqlPdlGPiGanglanprdf 223
                                         ivp++Ga++++telGr++veP+ei++iprG++f+v++ +e   +rGyi+e+ygakf+lPd+GPiGan+lanprdf
  lcl|FitnessBrowser__Smeli:SMc03208 169 IVPETGAIQVFTELGRMDVEPSEICLIPRGMMFKVTRLGEekvWRGYICENYGAKFTLPDRGPIGANCLANPRDF 243
                                         ************************************99544789******************************* PP

                           TIGR01015 224 eaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvlt 298
                                         ++Pvaa+edke+  ++rv+ k++g++++++++hspldvvawhGny+Pykydlk+f+ ++++ fdhpdPsiftvlt
  lcl|FitnessBrowser__Smeli:SMc03208 244 KTPVAAYEDKET--PCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVGAILFDHPDPSIFTVLT 316
                                         ************..99*********************************************************** PP

                           TIGR01015 299 apsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdvea 373
                                         aps +eGta++dfvifpPrwlvae+tfrPP+yhrn+msefmGli+G+ydakeeGfvpgG+slhn+m ahGPd+++
  lcl|FitnessBrowser__Smeli:SMc03208 317 APSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLIYGRYDAKEEGFVPGGMSLHNMMLAHGPDFSG 391
                                         *************************************************************************** PP

                           TIGR01015 374 fekasnaelkPekiddgtlafmfesslslavtklakelekldedyeevwqglkkkf 429
                                         fekasn+elkP k+d+ t+afmfe+++++++t++a+el++l++dy+++w+gl++kf
  lcl|FitnessBrowser__Smeli:SMc03208 392 FEKASNGELKPVKLDN-TMAFMFETRFPQQLTTFAAELDTLQDDYMDCWSGLERKF 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.84
//
[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