Alignments for a candidate for hmgA in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Paraburkholderia sp. CCGE1002

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_013091977.1 BC1002_RS20860 homogentisate 1,2-dioxygenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4962
         (434 letters)



>NCBI__GCF_000092885.1:WP_013091977.1
          Length = 434

 Score =  548 bits (1413), Expect = e-161
 Identities = 271/415 (65%), Positives = 321/415 (77%), Gaps = 4/415 (0%)

Query: 12  YQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEARRTWMYRIQPS 71
           Y SGFGN+FS+EA+PGALP G+NSPQ+AP+GL+ EL SG AFT  R+E RRTWMYRI PS
Sbjct: 12  YMSGFGNQFSTEAIPGALPEGRNSPQRAPHGLFAELLSGAAFTAPRAENRRTWMYRILPS 71

Query: 72  ANHPAFFKLDRQL-TGGPLGEV-TP-NRLRWNPLDIPAEPTDFIDGLVSMAANSGAEKPA 128
           A H A+ K+++     GP GEV TP NR RW+P   P  PTDF+DG V++A N   E  +
Sbjct: 72  AMHGAYRKIEQPAWESGPFGEVDTPANRFRWDPWPAPTLPTDFVDGTVTIAGNGSPEAQS 131

Query: 129 GISIYNYRANRSM-ERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVLPRGLKFR 187
           G++ + YRAN SM  R   NADGEML+VP+LGRL I TELGVL+L P E+AVLPRGL F 
Sbjct: 132 GMTAHMYRANASMANRYLLNADGEMLIVPQLGRLTIRTELGVLDLAPGEVAVLPRGLHFA 191

Query: 188 IELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPTTLVQKFL 247
           ++L D +A GY+AEN+GAP RLP+LGPIGSNGLAN RDFLTPVAAYE+ Q+   +V+KFL
Sbjct: 192 VDLDDGEASGYIAENYGAPFRLPELGPIGSNGLANHRDFLTPVAAYEDGQRNVKIVRKFL 251

Query: 248 GQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGL 307
           G+ W    NHSPLNVVAWHGN VPYKYDL RF  IGTVSFDHPDPSI+TVLTSP++V G 
Sbjct: 252 GKFWEGTQNHSPLNVVAWHGNLVPYKYDLARFMAIGTVSFDHPDPSIYTVLTSPSTVPGT 311

Query: 308 ANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGASLHSCMSA 367
           AN DFVIFPPRW+VAE TFRPPWFHRNLM+E MGL+ G YDAKAEGFVPGG SLH+CM  
Sbjct: 312 ANCDFVIFPPRWLVAEDTFRPPWFHRNLMSELMGLVYGVYDAKAEGFVPGGVSLHNCMMP 371

Query: 368 HGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDACW 422
           HGPD  T  KA + EL P KI NT+AFMFE+S+V + +R +L+    Q  YDA W
Sbjct: 372 HGPDAATFDKASSTELIPHKIANTLAFMFESSRVFKLTRSSLEAVNRQTGYDAVW 426


Lambda     K      H
   0.320    0.137    0.426 

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: 741
Number of extensions: 27
Number of successful extensions: 3
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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_013091977.1 BC1002_RS20860 (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.14406.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-199  648.1   0.0   3.4e-199  647.9   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013091977.1  BC1002_RS20860 homogentisate 1,2


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013091977.1  BC1002_RS20860 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.9   0.0  3.4e-199  3.4e-199       3     426 ..      11     430 ..       9     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.9 bits;  conditional E-value: 3.4e-199
                                 TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 
                                               +y+sGfgn+f++ea+pgalP+G+nsPq+ap+gl+ae lsG+aftaPraen+r+w+yri+Psa+h a+ +
  lcl|NCBI__GCF_000092885.1:WP_013091977.1  11 TYMSGFGNQFSTEAIPGALPEGRNSPQRAPHGLFAELLSGAAFTAPRAENRRTWMYRILPSAMHGAYRK 79 
                                               7****************************************************************9999 PP

                                 TIGR01015  72 lkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmed 140
                                               ++ +  + + +f e+++  n++rw+p ++p+   +dfv+g vt+ag+g +++++G+++h+y +nasm +
  lcl|NCBI__GCF_000092885.1:WP_013091977.1  80 IE-QPAWESGPFGEVDTPANRFRWDPWPAPT-LPTDFVDGTVTIAGNGSPEAQSGMTAHMYRANASMAN 146
                                               98.699************************7.99*********************************** PP

                                 TIGR01015 141 evfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPd 208
                                               +++ nadG++livpq G l+i+telG+l+++P+e+av+prG++f+v+++ +ea Gyi e+yga f+lP+
  lcl|NCBI__GCF_000092885.1:WP_013091977.1 147 RYLLNADGEMLIVPQLGRLTIRTELGVLDLAPGEVAVLPRGLHFAVDLDdGEASGYIAENYGAPFRLPE 215
                                               ************************************************9899***************** PP

                                 TIGR01015 209 lGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkk 277
                                               lGPiG+nglan rdf +Pvaa+ed +   +v++++kf gk++  +q+hspl+vvawhGn+vPykydl +
  lcl|NCBI__GCF_000092885.1:WP_013091977.1 216 LGPIGSNGLANHRDFLTPVAAYEDGQR--NVKIVRKFLGKFWEGTQNHSPLNVVAWHGNLVPYKYDLAR 282
                                               ************************998..89************************************** PP

                                 TIGR01015 278 fnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGky 346
                                               f++i++vsfdhpdPsi+tvlt+ps+ +Gta++dfvifpPrwlvae+tfrPP++hrn+mse mGl++G y
  lcl|NCBI__GCF_000092885.1:WP_013091977.1 283 FMAIGTVSFDHPDPSIYTVLTSPSTVPGTANCDFVIFPPRWLVAEDTFRPPWFHRNLMSELMGLVYGVY 351
                                               ********************************************************************* PP

                                 TIGR01015 347 dakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakelekld 415
                                               dak+eGfvpgG slhn+m +hGPd+++f+kas +el P+ki++ tlafmfess ++++t+ + e+ + +
  lcl|NCBI__GCF_000092885.1:WP_013091977.1 352 DAKAEGFVPGGVSLHNCMMPHGPDAATFDKASSTELIPHKIAN-TLAFMFESSRVFKLTRSSLEAVNRQ 419
                                               *******************************************.************************* PP

                                 TIGR01015 416 edyeevwqglk 426
                                               + y++vw+g+ 
  lcl|NCBI__GCF_000092885.1:WP_013091977.1 420 TGYDAVWDGFT 430
                                               ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (434 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: 10.87
//
[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