Alignments for a candidate for hmgA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas putida KT2440

Align homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate PP_4621 PP_4621 Homogentisate 1,2-dioxygenase

Query= BRENDA::Q88E47
         (433 letters)



>FitnessBrowser__Putida:PP_4621
          Length = 433

 Score =  899 bits (2322), Expect = 0.0
 Identities = 433/433 (100%), Positives = 433/433 (100%)

Query: 1   MNRDTSPDLHYLSGFGNEFASEALPGALPVGQNSPQKAPYGLYAELLSGTAFTMARSELR 60
           MNRDTSPDLHYLSGFGNEFASEALPGALPVGQNSPQKAPYGLYAELLSGTAFTMARSELR
Sbjct: 1   MNRDTSPDLHYLSGFGNEFASEALPGALPVGQNSPQKAPYGLYAELLSGTAFTMARSELR 60

Query: 61  RTWLYRIRPSALHPRFERLARQPLGGPLGGINPNRLRWSPQPIPAEPTDFIEGWLPMAAN 120
           RTWLYRIRPSALHPRFERLARQPLGGPLGGINPNRLRWSPQPIPAEPTDFIEGWLPMAAN
Sbjct: 61  RTWLYRIRPSALHPRFERLARQPLGGPLGGINPNRLRWSPQPIPAEPTDFIEGWLPMAAN 120

Query: 121 AGAEKPAGVSIYIYRANRSMERVFFNADGELLLVPEQGRLRIATELGVMEVEPLEIAVIP 180
           AGAEKPAGVSIYIYRANRSMERVFFNADGELLLVPEQGRLRIATELGVMEVEPLEIAVIP
Sbjct: 121 AGAEKPAGVSIYIYRANRSMERVFFNADGELLLVPEQGRLRIATELGVMEVEPLEIAVIP 180

Query: 181 RGMKFRVELLDGQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEEAEGPVQ 240
           RGMKFRVELLDGQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEEAEGPVQ
Sbjct: 181 RGMKFRVELLDGQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEEAEGPVQ 240

Query: 241 LVQKFLGEHWACELQHSPLDVVAWHGSNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSP 300
           LVQKFLGEHWACELQHSPLDVVAWHGSNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSP
Sbjct: 241 LVQKFLGEHWACELQHSPLDVVAWHGSNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSP 300

Query: 301 TSVHGMANMDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLINGAYDAKAEGFLPGGASL 360
           TSVHGMANMDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLINGAYDAKAEGFLPGGASL
Sbjct: 301 TSVHGMANMDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLINGAYDAKAEGFLPGGASL 360

Query: 361 HGVMSAHGPDAETCEKAIAADLAPHKIDNTMAFMFETSQVLRPSLQALECPQLQADYDSC 420
           HGVMSAHGPDAETCEKAIAADLAPHKIDNTMAFMFETSQVLRPSLQALECPQLQADYDSC
Sbjct: 361 HGVMSAHGPDAETCEKAIAADLAPHKIDNTMAFMFETSQVLRPSLQALECPQLQADYDSC 420

Query: 421 WATLPSTFNPNRR 433
           WATLPSTFNPNRR
Sbjct: 421 WATLPSTFNPNRR 433


Lambda     K      H
   0.320    0.138    0.434 

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: 928
Number of extensions: 28
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: 433
Length of database: 433
Length adjustment: 32
Effective length of query: 401
Effective length of database: 401
Effective search space:   160801
Effective search space used:   160801
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 PP_4621 PP_4621 (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.7921.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.9e-196  637.2   0.0   6.7e-196  637.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4621  PP_4621 Homogentisate 1,2-dioxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4621  PP_4621 Homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.0   0.0  6.7e-196  6.7e-196       2     429 .]       9     428 ..       8     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 637.0 bits;  conditional E-value: 6.7e-196
                           TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkese 76 
                                         l+ylsGfgnef+sea+pgalPvGqnsPqkapyglyae lsG+aft+ r+e +r+wlyrirPsa h  fe+l+   
  lcl|FitnessBrowser__Putida:PP_4621   9 LHYLSGFGNEFASEALPGALPVGQNSPQKAPYGLYAELLSGTAFTMARSELRRTWLYRIRPSALHPRFERLA--R 81 
                                         79****************************************************************999998..4 PP

                           TIGR01015  77 ekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdll 151
                                         + l  +      +pn+lrwsp +ip+ e +df+eg   +a+++ a++ aG+++++y +n sm ++vf+nadG+ll
  lcl|FitnessBrowser__Putida:PP_4621  82 QPLGGPLG--GINPNRLRWSPQPIPA-EPTDFIEGWLPMAANAGAEKPAGVSIYIYRANRSM-ERVFFNADGELL 152
                                         66666666..5689***********6.9**********************************.89********** PP

                           TIGR01015 152 ivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlGPiGanglanprdfea 225
                                         +vp++G l+i telG+++veP eiaviprG++frve+  ++arGyi e++ga  +lPdlGPiG+nglanprdf +
  lcl|FitnessBrowser__Putida:PP_4621 153 LVPEQGRLRIATELGVMEVEPLEIAVIPRGMKFRVELLdGQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLT 227
                                         ************************************99899********************************** PP

                           TIGR01015 226 PvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltap 300
                                         Pva +e+ e+  +v++++kf g+ +a++ +hspldvvawhG  vPykydl++fn+i++vsfdhpdPsiftvlt+p
  lcl|FitnessBrowser__Putida:PP_4621 228 PVAHYEEAEG--PVQLVQKFLGEHWACELQHSPLDVVAWHGSNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSP 300
                                         ********99..99************************************************************* PP

                           TIGR01015 301 sdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafe 375
                                         ++ +G+a++dfvifpPrw+vae+tfrPP++hrn+m efmGli+G+ydak+eGf pgGaslh +msahGPd+e+ e
  lcl|FitnessBrowser__Putida:PP_4621 301 TSVHGMANMDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLINGAYDAKAEGFLPGGASLHGVMSAHGPDAETCE 375
                                         *************************************************************************** PP

                           TIGR01015 376 kasnaelkPekiddgtlafmfesslslavtklakelekldedyeevwqglkkkf 429
                                         ka +a+l+P+kid+ t+afmfe+s +l+ + +a e+ +l++dy+++w +l + f
  lcl|FitnessBrowser__Putida:PP_4621 376 KAIAADLAPHKIDN-TMAFMFETSQVLRPSLQALECPQLQADYDSCWATLPSTF 428
                                         **************.*********************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (433 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: 00:00:00.02
# Mc/sec: 6.71
//
[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