Alignments for a candidate for PS417_12065 in Pseudomonas simiae WCS417

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 GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  319 bits (818), Expect = 1e-91
 Identities = 189/492 (38%), Positives = 284/492 (57%), Gaps = 3/492 (0%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           LL+ E++ K Y GV AL+   L +  G +HAL G NGAGKST + IL G+  +D G IL+
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G   QF    +A+AAGI ++ QE   IPY+T  ENI+LG E      ++  + +   + 
Sbjct: 64  DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEASE 123

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
            L   L   +D    +  LSVA+ Q VEIAKA + D +++++DEPT+ +   EA+ LF+ 
Sbjct: 124 ALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEI 183

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245
           +R L  QG  ++++SH L E+ Q+ D  S+ RDG  V    +AD D DHLV  +VG+ L 
Sbjct: 184 MRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243

Query: 246 -RIDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYG 304
                K  RE      L+V ++           QL +GEILG  GL+GSGR+E    + G
Sbjct: 244 CSFPPKPTRE-RGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGMMG 302

Query: 305 LTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLS 364
              + S  V L+G+ + +  P   +  G+ L+ E RK  GL+   SI  NI+L+   +  
Sbjct: 303 ALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQ 362

Query: 365 SWS-LINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423
           + S LI+  +E    E ++K+L IK  S E  V ++SGGNQQKVV+A+ ++     L+ D
Sbjct: 363 NASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFD 422

Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483
           EPTRGID GAK +IY L+      G A I++SSE PE++ + DR+AVF  G +V +   +
Sbjct: 423 EPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEAS 482

Query: 484 ALSQEALLRLAS 495
           A++ + ++R A+
Sbjct: 483 AVNPQEVMRHAT 494



 Score = 83.6 bits (205), Expect = 1e-20
 Identities = 62/244 (25%), Positives = 108/244 (44%), Gaps = 10/244 (4%)

Query: 4   PLLLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSI 63
           PLLL+ + +     G       R  L  G +    G  G+G++     +MG     +  +
Sbjct: 256 PLLLEVKDIQLVRNGP----HNRFQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDV 311

Query: 64  LLNGAPVQFNRPSEALAAGIAMITQELEP---IPYMTVAENIWLGREPR--RAGCIVDNK 118
            L G  +  + P++ALA GI ++ +  +    I   ++ ENI L   P+   A  ++D  
Sbjct: 312 WLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQNASGLIDKN 371

Query: 119 ALNRRTRELLDSLEFDVDAT-SPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEH 177
                   L+  L     ++ S +  LS    Q V IA+  +H C V++ DEPT  I   
Sbjct: 372 RECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVG 431

Query: 178 EAQTLFKAIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVR 237
               ++  +R LT QG  I+ +S  L E+  + D  ++F  GA V+    + ++   ++R
Sbjct: 432 AKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVMR 491

Query: 238 GIVG 241
              G
Sbjct: 492 HATG 495


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: 545
Number of extensions: 28
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: 495
Length of database: 502
Length adjustment: 34
Effective length of query: 461
Effective length of database: 468
Effective search space:   215748
Effective search space used:   215748
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources