Alignments for a candidate for hmgA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Cupriavidus basilensis 4G11

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate RR42_RS31275 RR42_RS31275 homogentisate 1,2-dioxygenase

Query= reanno::Cup4G11:RR42_RS31275
         (449 letters)



>FitnessBrowser__Cup4G11:RR42_RS31275
          Length = 449

 Score =  943 bits (2437), Expect = 0.0
 Identities = 449/449 (100%), Positives = 449/449 (100%)

Query: 1   MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60
           MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS
Sbjct: 1   MTQTQLNVVNVTGQAPDHGTPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQIS 60

Query: 61  GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120
           GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE
Sbjct: 61  GTAFTAPRAHNRRSWCYRIRAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKE 120

Query: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180
           PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE
Sbjct: 121 PTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATE 180

Query: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240
           MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF
Sbjct: 181 MGLLDVEPQEIVVIPRGVRFRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDF 240

Query: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300
           LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS
Sbjct: 241 LTPHAWYEDREGDFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSIS 300

Query: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360
           FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV
Sbjct: 301 FDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGV 360

Query: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420
           YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT
Sbjct: 361 YDAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPT 420

Query: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449
           PYAAESAQLQDDYYRCWQGLKKHFNPNER
Sbjct: 421 PYAAESAQLQDDYYRCWQGLKKHFNPNER 449


Lambda     K      H
   0.320    0.138    0.439 

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: 973
Number of extensions: 31
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: 449
Length of database: 449
Length adjustment: 33
Effective length of query: 416
Effective length of database: 416
Effective search space:   173056
Effective search space used:   173056
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 RR42_RS31275 RR42_RS31275 (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.633.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.9e-207  672.7   0.0   1.1e-206  672.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS31275  RR42_RS31275 homogentisate 1,2-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS31275  RR42_RS31275 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.5   0.0  1.1e-206  1.1e-206       3     429 .]      22     444 ..      20     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 672.5 bits;  conditional E-value: 1.1e-206
                                 TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 
                                                y+sGf nef++ea+pgalPvGqnsPq+apyglyaeq+sG+aftaPra+n+rsw yrir +a+he+f++
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275  22 GYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIRAAAMHEPFTR 90 
                                               59*****************************************************************99 PP

                                 TIGR01015  72 lkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmed 140
                                               ++  ++ ++++f+ ++++pnq+rwsp  +p+ e +dfv+g+ t+ag+g +++ +G ++hly++n sm+d
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275  91 VE--QSRIVSHFDAVPPSPNQMRWSPPAMPK-EPTDFVDGIITMAGNGGPEAMSGCGIHLYLANRSMTD 156
                                               99..789999********************5.9************************************ PP

                                 TIGR01015 141 evfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPd 208
                                               + fynadG++livpq+G l++ te+G l+veP+ei+viprGvrfrve+  +earGyi+e+yga f+lPd
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275 157 RFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVRFRVELPdGEARGYICENYGALFRLPD 225
                                               ************************************************9899***************** PP

                                 TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277
                                               lG iG+nglanprdf +P a++ed+e+  +++++ kfqg+l+ a ++hspldvvawhGny+Pykydl++
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275 226 LGVIGSNGLANPRDFLTPHAWYEDREG--DFELVAKFQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRR 292
                                               ***************************..9*************************************** PP

                                 TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346
                                               fn+i+s+sfdhpdPsif vl +psd++G+  +dfvif Prwl  ++tfrPP++hrn+ sefmGli+G y
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275 293 FNTIGSISFDHPDPSIFLVLQSPSDTPGVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVY 361
                                               ********************************************************************* PP

                                 TIGR01015 347 dakeeGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmfesslslavtklakelekl 414
                                               dak++Gf pgGaslhn+ms hGPd+e+f ka++a+  +P++i+d t+afmfe+  +++ t +a+e+++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275 362 DAKADGFSPGGASLHNCMSGHGPDAETFAKATAADTsQPHRIGD-TMAFMFETPAVIRPTPYAAESAQL 429
                                               *********************************98638******.************************ PP

                                 TIGR01015 415 dedyeevwqglkkkf 429
                                               ++dy+ +wqglkk+f
  lcl|FitnessBrowser__Cup4G11:RR42_RS31275 430 QDDYYRCWQGLKKHF 444
                                               **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (449 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.82
//
[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