Alignments for a candidate for hmgA in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Sinorhizobium fredii NGR234

Align Homogentisate 1,2-dioxygenase; HGDO; Homogentisate oxygenase; Homogentisic acid oxidase; Homogentisicase; EC 1.13.11.5 (characterized)
to candidate YP_002827494.1 NGR_c29980 homogentisate 1,2-dioxygenase

Query= SwissProt::Q9X4F5
         (453 letters)



>NCBI__GCF_000018545.1:YP_002827494.1
          Length = 453

 Score =  860 bits (2223), Expect = 0.0
 Identities = 401/450 (89%), Positives = 424/450 (94%), Gaps = 2/450 (0%)

Query: 1   MLEKAEKQRRAGSGQQRAAGYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS 60
           ML KAEK+  A + +  A  YMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS
Sbjct: 1   MLGKAEKRSEALAAE--ALAYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGS 58

Query: 61  PFTAPRGTNERSWLYRIRPSVRHTGRFRRVDYPHWKTAPHVGEHSLALGQLRWSPLPAPS 120
           PFTAPRGTNERSWLYRIRPSVRHTGRF ++DYPHWKTAPH+ EH+LALGQLRW+PLP P+
Sbjct: 59  PFTAPRGTNERSWLYRIRPSVRHTGRFAKIDYPHWKTAPHIAEHALALGQLRWNPLPEPT 118

Query: 121 EALDFLQGIRTMTTAGDALTQAGMAAHAYAFNADMVDDYFFNADGELLIVPETGAIQVFT 180
             L+FLQGIRTMTTAGD LTQ GMAAHAY FNADMVDDYFFNADGELLIVPE GA+QVFT
Sbjct: 119 GELNFLQGIRTMTTAGDVLTQVGMAAHAYVFNADMVDDYFFNADGELLIVPEMGALQVFT 178

Query: 181 ELGRMDVEPSEICLIPRGMMFKVTRLGEEKVWRGYICENYGAKFTLPDRGPIGANCLANP 240
           ELG+MDV PSEICL+PRG MFKV RLGEEK WRGYICENYGAKFTLPDRGPIGANCLANP
Sbjct: 179 ELGKMDVAPSEICLVPRGTMFKVARLGEEKAWRGYICENYGAKFTLPDRGPIGANCLANP 238

Query: 241 RDFKTPVAAYEDKETPCRVQVKWCGSFHMVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG 300
           RDFKTPVAA+EDKETPCRVQVKWCGSFH VEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG
Sbjct: 239 RDFKTPVAAFEDKETPCRVQVKWCGSFHTVEIGHSPLDVVAWHGNYAPYKYDLKTFSPVG 298

Query: 301 AILFDHPDPSIFTVLTAPSGEEGTANVDFVIFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 360
           AILFDHPDPSIFTVLTAPSGEEGTANVDFV+FPPRWLVAEHTFRPPWYHRNIMSEFMGLI
Sbjct: 299 AILFDHPDPSIFTVLTAPSGEEGTANVDFVLFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 358

Query: 361 YGRYDAKEEGFVPGGMSLHNMMLAHGPDFSGFEKASNGELKPVKLDNTMAFMFETRFPQQ 420
           +GRYDAKEEGFVPGGMSLHNMMLAHGPD SGFEKA+NGELKPVKLDNTMAFMFETRFPQQ
Sbjct: 359 HGRYDAKEEGFVPGGMSLHNMMLAHGPDTSGFEKATNGELKPVKLDNTMAFMFETRFPQQ 418

Query: 421 LTTFAAELDTLQDDYMDCWSGLERKFDGTP 450
           LT FAAEL+TLQDDY+DCW+GL ++F+GTP
Sbjct: 419 LTRFAAELETLQDDYIDCWAGLRKRFNGTP 448


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: 916
Number of extensions: 29
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 YP_002827494.1 NGR_c29980 (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.17660.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-224  729.9   0.0     5e-224  729.7   0.0    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827494.1  NGR_c29980 homogentisate 1,2-dio


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827494.1  NGR_c29980 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.7   0.0    5e-224    5e-224       2     429 .]      17     444 ..      16     444 .. 0.98

  Alignments for each domain:
  == domain 1  score: 729.7 bits;  conditional E-value: 5e-224
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               l+y++Gfgn+fe+e++pgalP+GqnsPqk++yglyaeqlsGs+ftaPr +n+rswlyrirPs++h++++
  lcl|NCBI__GCF_000018545.1:YP_002827494.1  17 LAYMPGFGNDFETESLPGALPQGQNSPQKCNYGLYAEQLSGSPFTAPRGTNERSWLYRIRPSVRHTGRF 85 
                                               78******************************************************************* PP

                                 TIGR01015  71 elkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasm 138
                                               ++ ++ +++ta++  e++ +++qlrw+pl+ p+  +++f++g++t+++agd+ ++ G+a+h+y +na+m
  lcl|NCBI__GCF_000018545.1:YP_002827494.1  86 AKIDYPHWKTAPHIAEHAlALGQLRWNPLPEPT-GELNFLQGIRTMTTAGDVLTQVGMAAHAYVFNADM 153
                                               ***********998777779************7.89********************************* PP

                                 TIGR01015 139 edevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee...arGyilevygakf 204
                                                d++f+nadG+llivp++Gal+++telG+++v+P+ei+++prG +f+v++ +e   +rGyi+e+ygakf
  lcl|NCBI__GCF_000018545.1:YP_002827494.1 154 VDDYFFNADGELLIVPEMGALQVFTELGKMDVAPSEICLVPRGTMFKVARLGEekaWRGYICENYGAKF 222
                                               *************************************************99444679************ PP

                                 TIGR01015 205 qlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPyky 273
                                               +lPd+GPiGan+lanprdf++Pvaafedke+  ++rv+ k++g++++++++hspldvvawhGny+Pyky
  lcl|NCBI__GCF_000018545.1:YP_002827494.1 223 TLPDRGPIGANCLANPRDFKTPVAAFEDKET--PCRVQVKWCGSFHTVEIGHSPLDVVAWHGNYAPYKY 289
                                               *******************************..99********************************** PP

                                 TIGR01015 274 dlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGli 342
                                               dlk+f+ ++++ fdhpdPsiftvltaps +eGta++dfv+fpPrwlvae+tfrPP+yhrn+msefmGli
  lcl|NCBI__GCF_000018545.1:YP_002827494.1 290 DLKTFSPVGAILFDHPDPSIFTVLTAPSGEEGTANVDFVLFPPRWLVAEHTFRPPWYHRNIMSEFMGLI 358
                                               ********************************************************************* PP

                                 TIGR01015 343 kGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakel 411
                                               +G+ydakeeGfvpgG+slhn+m ahGPd+++feka+n+elkP k+d+ t+afmfe+++++++t++a+el
  lcl|NCBI__GCF_000018545.1:YP_002827494.1 359 HGRYDAKEEGFVPGGMSLHNMMLAHGPDTSGFEKATNGELKPVKLDN-TMAFMFETRFPQQLTRFAAEL 426
                                               ***********************************************.********************* PP

                                 TIGR01015 412 ekldedyeevwqglkkkf 429
                                               e+l++dy ++w gl+k+f
  lcl|NCBI__GCF_000018545.1:YP_002827494.1 427 ETLQDDYIDCWAGLRKRF 444
                                               ***************987 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: 10.47
//
[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