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.17104.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: 00:00:00.02
# Mc/sec: 7.33
//
[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