GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TM1750 in Pseudomonas fluorescens FW300-N2E2

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf6N2E2_581 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)

Query= TCDB::Q9X272
         (328 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_581 Oligopeptide transport
           system permease protein OppB (TC 3.A.1.5.1)
          Length = 536

 Score =  251 bits (641), Expect = 3e-71
 Identities = 128/255 (50%), Positives = 180/255 (70%), Gaps = 8/255 (3%)

Query: 12  PLLQTVDLKKYFPQGKRI-------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64
           PLLQ  DLK +FP  K +       +KAVDGI   + +G+TLG+VGESG GKSTLG  IL
Sbjct: 274 PLLQVEDLKVWFPIKKGLFKRTVDYIKAVDGIRFSLPQGQTLGIVGESGSGKSTLGLAIL 333

Query: 65  KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
           +L+   GG I FEGK + +L  ++++P R++MQ++FQDP GSL+P+M V +I+ + L IH
Sbjct: 334 RLIGSQGG-IRFEGKQLDSLTQQQVRPLRREMQVVFQDPFGSLSPRMCVSQIVGEGLRIH 392

Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
           KIGT+ E+ + +   L  VG+  E  N +PHEFSGGQ+QRI IARAL L P  I+ DEP 
Sbjct: 393 KIGTEAEQEQAIIAALKEVGLDPETRNRYPHEFSGGQRQRIAIARALVLKPALILLDEPT 452

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           SALD ++Q Q+++LL  +Q K  ++YLFI+H+LAVV+ +SH++ V+  G++VE GD   I
Sbjct: 453 SALDRTVQRQVVELLRSLQTKYNLTYLFISHDLAVVKALSHQLMVVKHGQVVEQGDARSI 512

Query: 245 FLNPIHPYTRALLKS 259
           F  P HPYT+ LL++
Sbjct: 513 FAAPQHPYTQQLLEA 527



 Score =  194 bits (493), Expect = 4e-54
 Identities = 108/257 (42%), Positives = 165/257 (64%), Gaps = 8/257 (3%)

Query: 13  LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL----- 67
           L++  DL   F  G+R  + V+G+S +IK GETL LVGESG GKS    +IL+LL     
Sbjct: 6   LIEVRDLAVEFIVGERRQRVVEGVSFDIKRGETLALVGESGSGKSVTAHSILRLLPYPLA 65

Query: 68  RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
               G I + G+++  L +K ++  R  ++ +IFQ+P+ SLNP  ++ + I + L IHK 
Sbjct: 66  HHPTGTIQYAGQNLLGLKEKTIRHIRGNRIAMIFQEPMTSLNPLHSIEKQINEVLGIHKG 125

Query: 127 GTKKERRKRVEELLDMVGIGREF--INSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
            + K   +R  ELL++VGI      + + PHE SGGQ+QR+ IA ALA  P+ ++ DEP 
Sbjct: 126 LSGKVATRRTLELLELVGIPEPHKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           +ALDV++Q +I++LL+++Q ++G+S L I+H+L +V  I+H+V VM  G IVE    +++
Sbjct: 186 TALDVTVQLKILELLKQLQARLGMSLLLISHDLNLVRRIAHRVCVMQRGCIVEQASCEEL 245

Query: 245 FLNPIHPYTRALLKSVP 261
           F  P HPYTR LL + P
Sbjct: 246 FRAPQHPYTRELLGAEP 262


Lambda     K      H
   0.321    0.142    0.417 

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: 529
Number of extensions: 30
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 328
Length of database: 536
Length adjustment: 32
Effective length of query: 296
Effective length of database: 504
Effective search space:   149184
Effective search space used:   149184
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: 50 (23.9 bits)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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