GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_581
          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:

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