GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2C3

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_28510 AO356_28510 xylose transporter

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28510
          Length = 518

 Score =  340 bits (872), Expect = 7e-98
 Identities = 202/508 (39%), Positives = 313/508 (61%), Gaps = 27/508 (5%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDA--GEI 71
           +L+  GIVK F GV A++ +D +V   E V L GENGAGKSTL+K+L+ V       GEI
Sbjct: 5   LLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTWEGEI 64

Query: 72  LVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDEN 131
           + +G+ ++  S  +    GI +IHQEL L  +++VAENIF+ +E           R++  
Sbjct: 65  IWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLP-----GGRMNYP 119

Query: 132 YMYTRSKELL-DLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190
            M  R++ L+ +L     +    V       +Q+VEI KAL K+ R++ +DEP+S+LT  
Sbjct: 120 AMIHRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRS 179

Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250
           E E L +II  LK++G++ V++SH+LDEV  + D I V+RDGK I      + D+  II 
Sbjct: 180 EIEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIIT 239

Query: 251 MMVGREVEFF----PHGIETRPGEIALEVRNLKWKD-------KVKNVSFEVRKGEVLGF 299
            MVGRE+       PH I    GE+  E R++   D       +V ++SF +++GE+LG 
Sbjct: 240 QMVGREMSNLYPTEPHDI----GEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGI 295

Query: 300 AGLVGAGRTETMLLVFGVNQ-KESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLV 358
           AGLVGAGRTE +  +FG    +  G++++NG++++ + P  +I+ G+ ++PEDRK QG++
Sbjct: 296 AGLVGAGRTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGII 355

Query: 359 LRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQ 418
             + V  NI L  L   S+   +  E +   I ++ + R+ +KT S +    +LSGGNQQ
Sbjct: 356 PDLGVGQNITLAVLDNYSKLTRIDAEAELGSIDKE-IARMHLKTASPFLPITSLSGGNQQ 414

Query: 419 KVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLS 478
           K VLAK L T   +LI DEPTRG+DVGAK EI++++  LAA+G ++IM+SSEL E+L +S
Sbjct: 415 KAVLAKMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVS 474

Query: 479 DRIVVMWEGEITAVLDNREKRVTQEEIM 506
           DR++V+ +G++     N E  +TQE+++
Sbjct: 475 DRVLVIGDGQLRGDFINHE--LTQEQVL 500


Lambda     K      H
   0.319    0.138    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: 705
Number of extensions: 43
Number of successful extensions: 10
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: 520
Length of database: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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 (21.7 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