GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_2876 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2876
          Length = 525

 Score =  236 bits (601), Expect = 1e-66
 Identities = 122/251 (48%), Positives = 178/251 (70%), Gaps = 7/251 (2%)

Query: 13  LLQTVDLKKYFPQG------KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66
           +L+  +L+  FP G      K  L+AVDGIS+ I+ G+TLG+VGESG GKSTLG+ IL+L
Sbjct: 268 VLEVDNLQVRFPVGGGLFQRKTWLRAVDGISLNIQRGKTLGIVGESGSGKSTLGQAILRL 327

Query: 67  LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
           L  +GG I F+G+ +  L  K+++P+RKKMQ++FQDP GSL+P+M+V +II + L +H  
Sbjct: 328 LDSEGG-IRFQGQALDGLTQKQLRPWRKKMQVVFQDPFGSLSPRMSVAQIISEGLEVHSQ 386

Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186
            + +E    V   L+ VG+  +  + +PHEFSGGQ+QRI IARAL L P  I+ DEP SA
Sbjct: 387 LSTEECNAEVIRALNEVGLDPQSRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSA 446

Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246
           LD ++Q Q++ LL ++Q+K G++YLFI+H+LAVV  ++H + V+  GK+VE G   ++F 
Sbjct: 447 LDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVVRALAHDMIVIKDGKVVERGASHEVFD 506

Query: 247 NPIHPYTRALL 257
           +P HPYT+ LL
Sbjct: 507 SPQHPYTKELL 517



 Score =  173 bits (438), Expect = 1e-47
 Identities = 98/260 (37%), Positives = 163/260 (62%), Gaps = 11/260 (4%)

Query: 10  MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69
           M  L++  DL   F  G+ +++    + ++I+ GE L LVGESG GKS    +IL+LL  
Sbjct: 1   MTNLIEIRDLSVAF-SGQTVVR---NLCLDIRPGECLALVGESGSGKSVTAHSILQLLPQ 56

Query: 70  DG----GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
                 G I + G+++   +  +++  R  ++ +IFQ+P+ SLNP  ++ + I + L++H
Sbjct: 57  TDTETTGSIRYRGQELVGADAGKLRKLRGNRIAMIFQEPMTSLNPLHSIEKQIGETLLVH 116

Query: 125 KIGTKKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182
           K    K  + R+ ELL +VGI +  E + ++PH+ SGGQ+QR+ IA ALA  P+ ++ DE
Sbjct: 117 KGLAGKAAQARILELLHLVGIQKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADE 176

Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242
           P +ALDV++Q +I+ LL+ +QQ++G+S L I+H+L +V  I+ +V VM  G+IVE    +
Sbjct: 177 PTTALDVTVQRKILLLLKSLQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCE 236

Query: 243 KIFLNPIHPYTRALLKSVPK 262
            +F  P HPY+  LL + P+
Sbjct: 237 TLFTEPRHPYSCILLHAEPE 256


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: 513
Number of extensions: 13
Number of successful extensions: 5
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: 525
Length adjustment: 31
Effective length of query: 297
Effective length of database: 494
Effective search space:   146718
Effective search space used:   146718
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