Alignments for a candidate for hmgA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Stenotrophomonas chelatiphaga DSM 21508

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_057509091.1 ABB28_RS13360 homogentisate 1,2-dioxygenase

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



>NCBI__GCF_001431535.1:WP_057509091.1
          Length = 432

 Score =  652 bits (1682), Expect = 0.0
 Identities = 305/423 (72%), Positives = 346/423 (81%)

Query: 22  GYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIRA 81
           GYQ+GF NEFA+EA  GALP+GQN+PQ   +GLYAEQ+SGTAFTAPR  NRRSW YRIR 
Sbjct: 9   GYQTGFGNEFASEARAGALPIGQNAPQTVAHGLYAEQLSGTAFTAPRGSNRRSWLYRIRP 68

Query: 82  AAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKEPTDFVDGIITMAGNGGPEAMS 141
           A  H  FT   Q R+   F  +P SPNQ+RWSP  +P+ PTDF++G+ TM GNGGPEA +
Sbjct: 69  AVTHGEFTAFAQDRLQGSFHGLPASPNQLRWSPLPLPEAPTDFIEGLYTMGGNGGPEAHA 128

Query: 142 GCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVRFR 201
           G  IHLY ANR M  R+FYNADGE+LIVPQ GRLRL TEMG+++VEPQ+I VIPRGVRFR
Sbjct: 129 GVAIHLYAANRDMQGRYFYNADGELLIVPQLGRLRLLTEMGVVEVEPQQIAVIPRGVRFR 188

Query: 202 VELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAKFQ 261
           VELPDG+ARGY+CEN+GAL +LPDLG IGSNGLANPRDF TP A +ED +G+FELVAKF+
Sbjct: 189 VELPDGQARGYVCENFGALLKLPDLGPIGSNGLANPRDFETPQAAFEDLDGEFELVAKFE 248

Query: 262 GNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTPGV 321
           G LWRA I HSPLDVVAWHGNYAPY+YDLRRFNTIGSISFDHPDPSIFLVL SPSDT G 
Sbjct: 249 GQLWRARIDHSPLDVVAWHGNYAPYRYDLRRFNTIGSISFDHPDPSIFLVLHSPSDTAGT 308

Query: 322 DSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCMSG 381
            ++DF IF PRWL  Q+TFRPPWFHRNIASEFMGL+ G YDAKA+GF PGGASLHNCMSG
Sbjct: 309 SNMDFAIFPPRWLVAQHTFRPPWFHRNIASEFMGLVHGAYDAKAEGFVPGGASLHNCMSG 368

Query: 382 HGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQGLK 441
           HGPDA TF KA+AAD S+P  I DTMAFMFET  VIRPT  A  +A  Q DY +CW GL+
Sbjct: 369 HGPDAPTFDKASAADLSRPDVIKDTMAFMFETRGVIRPTAQALSAAHRQGDYQQCWNGLR 428

Query: 442 KHF 444
            +F
Sbjct: 429 NNF 431


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: 794
Number of extensions: 25
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: 432
Length adjustment: 32
Effective length of query: 417
Effective length of database: 400
Effective search space:   166800
Effective search space used:   166800
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_057509091.1 ABB28_RS13360 (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.6912.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-204  665.8   0.0   1.4e-204  665.6   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509091.1  ABB28_RS13360 homogentisate 1,2-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509091.1  ABB28_RS13360 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.6   0.0  1.4e-204  1.4e-204       3     429 .]       9     431 ..       7     431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 665.6 bits;  conditional E-value: 1.4e-204
                                 TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 
                                                y++Gfgnef+sea +galP Gqn+Pq +++glyaeqlsG+aftaPr +n+rswlyrirP+++h +f++
  lcl|NCBI__GCF_001431535.1:WP_057509091.1   9 GYQTGFGNEFASEARAGALPIGQNAPQTVAHGLYAEQLSGTAFTAPRGSNRRSWLYRIRPAVTHGEFTA 77 
                                               6******************************************************************99 PP

                                 TIGR01015  72 lkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmed 140
                                               ++  ++ l  +f++ +++pnqlrwspl++p+ + +df+egl+t++g+g ++++aG+a+hlya+n +m+ 
  lcl|NCBI__GCF_001431535.1:WP_057509091.1  78 FA--QDRLQGSFHGLPASPNQLRWSPLPLPE-APTDFIEGLYTMGGNGGPEAHAGVAIHLYAANRDMQG 143
                                               99..7899999*******************5.99*********************************** PP

                                 TIGR01015 141 evfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPd 208
                                               ++fynadG+llivpq G l++ te+G+++veP++iaviprGvrfrve+  ++arGy++e++ga  +lPd
  lcl|NCBI__GCF_001431535.1:WP_057509091.1 144 RYFYNADGELLIVPQLGRLRLLTEMGVVEVEPQQIAVIPRGVRFRVELPdGQARGYVCENFGALLKLPD 212
                                               ************************************************9899***************** PP

                                 TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277
                                               lGPiG+nglanprdfe+P aafed ++  e++++ kf+g+l+ a++dhspldvvawhGny+Py+ydl++
  lcl|NCBI__GCF_001431535.1:WP_057509091.1 213 LGPIGSNGLANPRDFETPQAAFEDLDG--EFELVAKFEGQLWRARIDHSPLDVVAWHGNYAPYRYDLRR 279
                                               ***************************..9*************************************** PP

                                 TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346
                                               fn+i+s+sfdhpdPsif vl +psd++Gt+++df ifpPrwlva++tfrPP++hrn+ sefmGl++G+y
  lcl|NCBI__GCF_001431535.1:WP_057509091.1 280 FNTIGSISFDHPDPSIFLVLHSPSDTAGTSNMDFAIFPPRWLVAQHTFRPPWFHRNIASEFMGLVHGAY 348
                                               ********************************************************************* PP

                                 TIGR01015 347 dakeeGfvpgGaslhnimsahGPdveafekasnaelk.Pekiddgtlafmfesslslavtklakelekl 414
                                               dak+eGfvpgGaslhn+ms hGPd+ +f+kas+a+l  P+ i+d t+afmfe++ +++ t +a ++++ 
  lcl|NCBI__GCF_001431535.1:WP_057509091.1 349 DAKAEGFVPGGASLHNCMSGHGPDAPTFDKASAADLSrPDVIKD-TMAFMFETRGVIRPTAQALSAAHR 416
                                               ************************************63777777.************************ PP

                                 TIGR01015 415 dedyeevwqglkkkf 429
                                               + dy+++w+gl+++f
  lcl|NCBI__GCF_001431535.1:WP_057509091.1 417 QGDYQQCWNGLRNNF 431
                                               ************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (432 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.50
//
[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