Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N1B4

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate Pf1N1B4_1025 Homogentisate 1,2-dioxygenase (EC 1.13.11.5)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025
          Length = 434

 Score =  865 bits (2236), Expect = 0.0
 Identities = 415/434 (95%), Positives = 423/434 (97%)

Query: 1   MNPDSTTPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60
           MN DST PALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTM RSEA
Sbjct: 1   MNLDSTAPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMTRSEA 60

Query: 61  RRTWMYRIQPSANHPAFFKLDRQLTGGPLGEVTPNRLRWNPLDIPAEPTDFIDGLVSMAA 120
           RRTWMYRIQPSANHPAF KLDRQL GGPLGEVTPNRLRWNPLD+P EPTDFIDGLVSMAA
Sbjct: 61  RRTWMYRIQPSANHPAFVKLDRQLAGGPLGEVTPNRLRWNPLDMPTEPTDFIDGLVSMAA 120

Query: 121 NSGAEKPAGISIYNYRANRSMERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVL 180
           NSGAEKP+GISIYNYRANRSMER FFNADGE+LLVP+LGRLRIATELGVLELEPLEIAVL
Sbjct: 121 NSGAEKPSGISIYNYRANRSMERVFFNADGELLLVPQLGRLRIATELGVLELEPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPT 240
           PRGLKFR+ELLDPQARGY+AENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YENL+QPT
Sbjct: 181 PRGLKFRVELLDPQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLKQPT 240

Query: 241 TLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           TLVQKFLGQLW CEL+HSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGQLWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDA 420
           LHSCMSAHGPDGETCTKAINAEL PAKIDNTMAFMFETSQVLRPSRFALDCPQLQN YDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINAELAPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 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: 912
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 Pf1N1B4_1025 (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.10287.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.4e-195  636.0   0.0   1.5e-195  635.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025  Homogentisate 1,2-dioxygenase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025  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 !  635.8   0.0  1.5e-195  1.5e-195       2     428 ..      10     428 ..       9     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 635.8 bits;  conditional E-value: 1.5e-195
                                      TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaa 65 
                                                    l+y+sGfgnef+sea+pgalPvGqnsPqkapygly+e +sG+aft+ r+e +r+w+yri+Psa+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025  10 LAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMTRSEARRTWMYRIQPSAN 73 
                                                    78************************************************************** PP

                                      TIGR01015  66 heafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlav 129
                                                    h af++l+   +    +    +++pn+lrw+pl++p+ e +df++glv++a+++ a++ +G+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025  74 HPAFVKLD--RQLAGGPLG--EVTPNRLRWNPLDMPT-EPTDFIDGLVSMAANSGAEKPSGISI 132
                                                    *****999..455555555..5679***********7.99************************ PP

                                      TIGR01015 130 hlyavnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee.a 192
                                                    + y +n sm ++vf+nadG+ll+vpq G l+i telG+l++eP eiav+prG++frve+ ++ a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 133 YNYRANRSM-ERVFFNADGELLLVPQLGRLRIATELGVLELEPLEIAVLPRGLKFRVELLDPqA 195
                                                    *********.89***********************************************96559 PP

                                      TIGR01015 193 rGyilevygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdh 256
                                                    rGyi e++ga  +lPdlGPiG+nglanprdf +Pva +e+ +   ++++++kf g+l+ ++ dh
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 196 RGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLKQ--PTTLVQKFLGQLWGCELDH 257
                                                    ***************************************9988..88***************** PP

                                      TIGR01015 257 spldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlv 320
                                                    spl+vvawhGn vPykydl++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifpPrw+v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 258 SPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFPPRWMV 321
                                                    **************************************************************** PP

                                      TIGR01015 321 aektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkP 384
                                                    aektfrPP++hrn+m efmGli+G+ydak+eGfvpgGaslh++msahGPd e+  ka nael+P
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 322 AEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGASLHSCMSAHGPDGETCTKAINAELAP 385
                                                    **************************************************************** PP

                                      TIGR01015 385 ekiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428
                                                     kid+ t+afmfe+s +l+ +++a  + +l+++y+++w +l   
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 386 AKIDN-TMAFMFETSQVLRPSRFALDCPQLQNNYDACWATLPAT 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.57
//
[ok]

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

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Candidates (tab-delimited)
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