Alignments for a candidate for hmgA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas fluorescens GW456-L13

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate PfGW456L13_4962 Homogentisate 1,2-dioxygenase (EC 1.13.11.5)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962
          Length = 434

 Score =  897 bits (2319), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MNPDSTTPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60
           MNPDSTTPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA
Sbjct: 1   MNPDSTTPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIQPSANHPAFFKLDRQLTGGPLGEVTPNRLRWNPLDIPAEPTDFIDGLVSMAA 120
           RRTWMYRIQPSANHPAFFKLDRQLTGGPLGEVTPNRLRWNPLDIPAEPTDFIDGLVSMAA
Sbjct: 61  RRTWMYRIQPSANHPAFFKLDRQLTGGPLGEVTPNRLRWNPLDIPAEPTDFIDGLVSMAA 120

Query: 121 NSGAEKPAGISIYNYRANRSMERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVL 180
           NSGAEKPAGISIYNYRANRSMERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVL
Sbjct: 121 NSGAEKPAGISIYNYRANRSMERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPT 240
           PRGLKFRIELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPT
Sbjct: 181 PRGLKFRIELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPT 240

Query: 241 TLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           TLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDA 420
           LHSCMSAHGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDA 420

Query: 421 CWATLPATFDPTRR 434
           CWATLPATFDPTRR
Sbjct: 421 CWATLPATFDPTRR 434


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: 936
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: 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 PfGW456L13_4962 (Homogentisate 1,2-dioxygenase (EC 1.13.11.5))
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.16872.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     6e-196  637.2   0.0   6.8e-196  637.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962  Homogentisate 1,2-dioxygenase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962  Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.0   0.0  6.8e-196  6.8e-196       2     428 ..      10     428 ..       9     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 637.0 bits;  conditional E-value: 6.8e-196
                                               TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrsw 56 
                                                             l+y+sGfgnef+sea+pgalPvGqnsPqkapygly+e +sG+aft+ r+e +r+w
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962  10 LAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEARRTW 64 
                                                             78***************************************************** PP

                                               TIGR01015  57 lyrirPsaaheafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveg 111
                                                             +yri+Psa+h af++l+   + +  +    +++pn+lrw+pl+ip+ e +df++g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962  65 MYRIQPSANHPAFFKLD--RQLTGGPLG--EVTPNRLRWNPLDIPA-EPTDFIDG 114
                                                             **************999..456666665..5569***********6.9******* PP

                                               TIGR01015 112 lvtlagagdaksraGlavhlyavnasmedevfynadGdllivpqkGaleittelG 166
                                                             lv++a+++ a++ aG++++ y +n sm +++f+nadG++l+vp+ G l+i telG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 115 LVSMAANSGAEKPAGISIYNYRANRSM-ERAFFNADGEMLLVPELGRLRIATELG 168
                                                             ***************************.89************************* PP

                                               TIGR01015 167 rlkvePneiaviprGvrfrveveee.arGyilevygakfqlPdlGPiGanglanp 220
                                                             +l++eP eiav+prG++fr+e+ ++ arGy+ e++ga  +lPdlGPiG+nglanp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 169 VLELEPLEIAVLPRGLKFRIELLDPqARGYVAENHGAPLRLPDLGPIGSNGLANP 223
                                                             **********************96559**************************** PP

                                               TIGR01015 221 rdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydl 275
                                                             rdf +Pvaa+e+ +   ++++++kf g+l+a++ +hspl+vvawhGn vPykydl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 224 RDFLTPVAAYENLQQ--PTTLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDL 276
                                                             ************999..88************************************ PP

                                               TIGR01015 276 kkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyy 330
                                                             ++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifpPrw+vaektfrPP++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 277 RRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFPPRWMVAEKTFRPPWF 331
                                                             ******************************************************* PP

                                               TIGR01015 331 hrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPe 385
                                                             hrn+m efmGli+G+ydak+eGfvpgGaslh++msahGPd e+  ka naelkP 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 332 HRNLMNEFMGLIQGEYDAKAEGFVPGGASLHSCMSAHGPDGETCTKAINAELKPA 386
                                                             ******************************************************* PP

                                               TIGR01015 386 kiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428
                                                             kid+ t+afmfe+s +l+ +++a  + +l++ y+++w +l   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4962 387 KIDN-TMAFMFETSQVLRPSRFALDCPQLQNTYDACWATLPAT 428
                                                             ****.*********************************99866 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.60
//
[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