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.3927702.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.71
//
[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:

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