GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araVsh in Pseudomonas simiae WCS417

Align ABC transporter related (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  363 bits (933), Expect = e-105
 Identities = 194/492 (39%), Positives = 313/492 (63%), Gaps = 7/492 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE+  ISK +PGV AL DV LR+  G V AL+GENGAGKSTL+K++ G    D G+I  
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEP-RRLGLIHFKKMYADAR 122
            G+P  F TP+ AQKAGI+ ++QE+NL+P++++A+N+++G E    L +++ ++M+    
Sbjct: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142

Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
            +L + ++++D    + + SIA +Q++ IA+ V+  + +L++DEPT+++  KEV  LF I
Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           +  LK++G  IV+ITH +++V+ I+D + V R+G +IG      +    LI  M+GR L 
Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
            QL   +E     T    +LL++ D+++ G  + ++  +  G+ +G+AGL+GSGR+ V  
Sbjct: 263 -QLFPLRE-----TPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAE 316

Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362
            +FG+    SG I L G+ + +S P  AI  G AL  EDRK+ G+   LS+ EN+ +A+ 
Sbjct: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL 376

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
                  ++     + + +    KL++ TP  ++ I+ LSGGNQQK +LARWL   P LL
Sbjct: 377 PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLL 436

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482
           +LDEPTRGID+GA AEI +LI  L  EGM++++ SSEL E++  S++V+V+ +   +  L
Sbjct: 437 ILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTL 496

Query: 483 SGAELTSQHVMQ 494
             +E T + VMQ
Sbjct: 497 DRSEATQEKVMQ 508



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 58/228 (25%), Positives = 109/228 (47%), Gaps = 14/228 (6%)

Query: 21  EDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQKAG 80
           +DVS  L AGE+  + G  G+G++ + + + G      G I   G+    + P  A + G
Sbjct: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348

Query: 81  ISTVYQE---VNLVPNLTVAQNLFLGYEPRRLG--LIHFKKMYADARAVLTQFKLDIDVS 135
            + + ++     L P L+V +N+ +   P   G   I  K +    RA+       + V 
Sbjct: 349 FALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKAL----RALCEDMCKKLRVK 404

Query: 136 APLSDYSIAV-----QQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190
            P  +  I       QQ   +AR +  + ++L+LDEPT  +D      ++ ++  L ++G
Sbjct: 405 TPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEG 464

Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG 238
           +A++ I+  L +V  +SDR+ V+  G+ +G    +E  Q K+++   G
Sbjct: 465 MAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512


Lambda     K      H
   0.319    0.136    0.377 

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: 548
Number of extensions: 25
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: 499
Length of database: 517
Length adjustment: 34
Effective length of query: 465
Effective length of database: 483
Effective search space:   224595
Effective search space used:   224595
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