Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2E2

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate Pf6N2E2_5290 Homogentisate 1,2-dioxygenase (EC 1.13.11.5)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5290
         (434 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290
          Length = 434

 Score =  899 bits (2323), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MNLVSPASDLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEA 60
           MNLVSPASDLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEA
Sbjct: 1   MNLVSPASDLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAA 120
           RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAA
Sbjct: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAA 120

Query: 121 NAGADKPAGISLYQYQANRSMERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVL 180
           NAGADKPAGISLYQYQANRSMERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVL
Sbjct: 121 NAGADKPAGISLYQYQANRSMERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVL 180

Query: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPT 240
           PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPT
Sbjct: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPT 240

Query: 241 SLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           SLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 SLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGAS
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGAS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420
           LHSCMSAHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420

Query: 421 CWASLPVTFDPTRR 434
           CWASLPVTFDPTRR
Sbjct: 421 CWASLPVTFDPTRR 434


Lambda     K      H
   0.321    0.138    0.435 

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: 938
Number of extensions: 21
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 Pf6N2E2_5290 (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.14012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.2e-195  634.1   0.0   5.9e-195  633.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290  Homogentisate 1,2-dioxygenase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290  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 !  633.9   0.0  5.9e-195  5.9e-195       2     427 ..      10     427 ..       9     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 633.9 bits;  conditional E-value: 5.9e-195
                                      TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaa 65 
                                                    l+y+sGfgnef+sea+pgalPvGqnsPqk+pyglyae +sG+aft+ r+e +r+w+yrirPsa+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290  10 LAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEARRTWMYRIRPSAN 73 
                                                    79************************************************************** PP

                                      TIGR01015  66 heafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlav 129
                                                    h af++l+   +    +    +++pn+lrw+pleip+ e +df++glv +a+++ a + aG+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290  74 HPAFTRLE--RQLAGGPLG--EVTPNRLRWNPLEIPA-EPTDFIDGLVCMAANAGADKPAGISL 132
                                                    **999998..455555555..5679***********6.9************************* PP

                                      TIGR01015 130 hlyavnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee.a 192
                                                    ++y++n sm ++vf+nadG+ livpq G l+ittelG+l+++P ei+v+prG++fr+e+ ++ a
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290 133 YQYQANRSM-ERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVLPRGLKFRIELLDPqA 195
                                                    *********.89***********************************************96559 PP

                                      TIGR01015 193 rGyilevygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdh 256
                                                    rGy+ e++ga  +lPdlGPiG+nglanprdf +Pva +e+     ++ +++kf g+l+ ++ dh
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290 196 RGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQ--PTSLVQKFLGELWGCELDH 257
                                                    ***************************************9988..88***************** PP

                                      TIGR01015 257 spldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlv 320
                                                    spldvvawhGn vPykydl++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifpPrw+v
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290 258 SPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFPPRWMV 321
                                                    **************************************************************** PP

                                      TIGR01015 321 aektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkP 384
                                                    ae+tfrPP++hrn+m efmGli+G+ydak+eGf pgGaslh++msahGPd e+  ka nael+P
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290 322 AENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGASLHSCMSAHGPDGETCTKAINAELQP 385
                                                    **************************************************************** PP

                                      TIGR01015 385 ekiddgtlafmfesslslavtklakelekldedyeevwqglkk 427
                                                     kid+ t+afmfe+s +l+ +++a  + +l++dy+++w +l  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5290 386 VKIDN-TMAFMFETSQVLRPSRFALDCPQLQTDYDACWASLPV 427
                                                    *****.*********************************9975 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.18
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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