GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12065 in Pseudomonas simiae WCS417

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3594 PS417_18400 sugar ABC transporter ATPase

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__WCS417:GFF3594
          Length = 517

 Score =  323 bits (829), Expect = 7e-93
 Identities = 198/494 (40%), Positives = 287/494 (58%), Gaps = 10/494 (2%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           +L    + K YA  P L D  L+L  G V AL G NGAGKST   I+ G+     G +  
Sbjct: 9   VLSVSGIGKTYAQ-PVLSDITLTLNRGEVLALTGENGAGKSTLSKIIGGLVTPTTGHMQF 67

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           NG   +    ++A   G+ M+ QEL  +P +TVAEN++L   P   G I   K L +   
Sbjct: 68  NGQDFRPGSRTQAEELGVRMVMQELNLLPTLTVAENLFLDNLPSHCGWI-SRKQLRKAAI 126

Query: 126 ELLDSLEFD-VDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184
           E +  +  D +D  + +  L +   Q+VEIA+    DC V+I+DEPT+ +   E + LF+
Sbjct: 127 EAMAQVGLDAIDPDTLVGSLGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186

Query: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244
            I RL A+G  I+Y+SHRL ELA++A   ++ RDG  V    MA+ + + LV  +VG+EL
Sbjct: 187 QITRLQARGVAIIYISHRLEELARVAQRIAVLRDGKLVCVEPMANYNSEQLVTLMVGREL 246

Query: 245 -TRIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303
              ID  +G        L V  L+R+ +  D+S ++R GEI GI GL+G+GR+E L  I+
Sbjct: 247 GEHID--LGPRTIGGPALTVKGLTRSDKVRDVSFEVRAGEIYGISGLIGAGRTELLRLIF 304

Query: 304 GLTVADSGSVTLQGKP---MPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAY 360
           G  +ADSG+V L G P   + I  P   +  G++L+TEDRK  GL+LT SI +NIAL   
Sbjct: 305 GADLADSGTVAL-GSPAQVVSIRSPVDAVGHGIALITEDRKGEGLLLTQSISANIALGNM 363

Query: 361 KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420
             +S   ++N+R ET LA+  +  ++I+++S    V+ +SGGNQQKVV+ + L  +   +
Sbjct: 364 PEISGGGVVNSRDETALAKRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERDCSVM 423

Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIS 480
           L DEPTRGID GAK +IY LL +  R G A +VVSS+  EL+ + DRI V   GRL+   
Sbjct: 424 LFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIETF 483

Query: 481 TDTALSQEALLRLA 494
              + +Q+ LL  A
Sbjct: 484 ERDSWTQDELLAAA 497


Lambda     K      H
   0.319    0.135    0.381 

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: 605
Number of extensions: 27
Number of successful extensions: 9
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: 495
Length of database: 517
Length adjustment: 34
Effective length of query: 461
Effective length of database: 483
Effective search space:   222663
Effective search space used:   222663
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: 52 (24.6 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