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.31256.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.47
//
[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:

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:

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:

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:

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