GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Pseudomonas simiae WCS417

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 GFF2391 PS417_12190 microcin ABC transporter ATP-binding protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__WCS417:GFF2391
          Length = 531

 Score =  241 bits (616), Expect = 2e-68
 Identities = 124/255 (48%), Positives = 178/255 (69%), Gaps = 8/255 (3%)

Query: 12  PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64
           PLL+  +LK +FP  K  L       KAVDGI+  + +G+TLG+VGESG GKSTLG  IL
Sbjct: 274 PLLEVDNLKVWFPIKKGFLRNTVDYVKAVDGINFSLPQGQTLGIVGESGSGKSTLGLAIL 333

Query: 65  KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
           +L+   GG I FEG+ +  L+ ++++P R++MQ++FQDP GSL+P+M V  I+ + L IH
Sbjct: 334 RLIASKGG-IRFEGQQLDTLSQQQVRPLRREMQVVFQDPFGSLSPRMCVSEIVGEGLRIH 392

Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
           K+GT  E+   +   L  VG+  E  + +PHEFSGGQ+QRI IARAL L P+ I+ DEP 
Sbjct: 393 KMGTPAEQEAAIIAALKEVGLDPESRHRYPHEFSGGQRQRIAIARALVLKPRLILLDEPT 452

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

Query: 245 FLNPIHPYTRALLKS 259
           F  P H YTR LL++
Sbjct: 513 FAAPQHGYTRQLLEA 527



 Score =  194 bits (493), Expect = 4e-54
 Identities = 107/257 (41%), Positives = 163/257 (63%), Gaps = 8/257 (3%)

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

Query: 68  RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
           R   G I + G+D+  L +K ++  R  ++ +IFQ+P+ SLNP  ++ + I + L +HK 
Sbjct: 66  RHPSGTINYAGQDLLTLKEKTIRHIRGNRIAMIFQEPMTSLNPLHSIEKQINEVLGLHKG 125

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

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           +ALDV++Q +I++LL+E+Q ++G++ L I+H+L +V  I+H+V VM  G IVE  D + +
Sbjct: 186 TALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQKGCIVEQADCETL 245

Query: 245 FLNPIHPYTRALLKSVP 261
           F +P HPYT+ LL + P
Sbjct: 246 FQSPQHPYTQELLAAEP 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: 492
Number of extensions: 26
Number of successful extensions: 7
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: 531
Length adjustment: 31
Effective length of query: 297
Effective length of database: 500
Effective search space:   148500
Effective search space used:   148500
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