Alignments for a candidate for araVsh in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Klebsiella michiganensis M5al

Align ABC transporter related (characterized, see rationale)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  371 bits (953), Expect = e-107
 Identities = 196/472 (41%), Positives = 307/472 (65%), Gaps = 7/472 (1%)

Query: 5   LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64
           LE + ISK +PGVKAL++VSLR+  G VHAL+GENGAGKSTL+K + G    D G I   
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 65  GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124
           GEP  F   MDA ++GIS ++QE+NLVP++TVA+N++LG EP + G +  +++    + +
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125

Query: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184
           L +  + +     + + SIA QQ++ IA+ V+ +A ++++DEPT++L   EV  LF I+ 
Sbjct: 126 LDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIR 185

Query: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQEQ 244
            L+ +G AI++I+H +D+++ I+D I+V R+G ++G   T E  +  LI  M+GR L  Q
Sbjct: 186 DLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGREL-TQ 244

Query: 245 LVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAV 304
           L  K             +L++ ++S KG+   +N +V +G+ +G+AGL+G+GRSEV  ++
Sbjct: 245 LFPKFN-----NAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESL 299

Query: 305 FGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-ILALQA 363
           FG++  DSG + + G  +N+  P  AI  G+AL  EDRK  G+   LS+ EN+ I+ +  
Sbjct: 300 FGMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPE 359

Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423
            IG   ++ + +  E     I +L I TP  D+ I  LSGGNQQKV++ARWL  +P +L+
Sbjct: 360 YIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILI 419

Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475
           LDEPTRGID+GA AEI  LI  L + G+++++ SSEL E++  S++V+V+ +
Sbjct: 420 LDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHE 471



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 54/210 (25%), Positives = 109/210 (51%), Gaps = 9/210 (4%)

Query: 19  ALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMDAQK 78
           A  D++  +  GE+  + G  GAG+S +++ + G +  D G++L  G P + ++P  A +
Sbjct: 268 AFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEVLIDGMPVNIDSPSTAIE 327

Query: 79  AGISTVYQE---VNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFKLDIDVS 135
            G++ + ++     L   L+V +N+ +   P  +G   F +    A   + Q +  +++ 
Sbjct: 328 KGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHLKMAEDCMEQIRR-LNIK 386

Query: 136 APLSDYSI-----AVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKAKG 190
            P  D  I       QQ + IAR +    K+L+LDEPT  +D      ++ ++++L  +G
Sbjct: 387 TPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDVGAKAEIYHLISELANRG 446

Query: 191 VAIVFITHFLDQVYQISDRITVLRNGQFIG 220
           VA++ ++  L ++  +SDR+ V+  G+  G
Sbjct: 447 VAVIMVSSELPEILGMSDRVMVMHEGRITG 476



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 57/222 (25%), Positives = 116/222 (52%), Gaps = 8/222 (3%)

Query: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332
           ++ +++L V  G    L G  G+G+S +   + G+   D G+I + G+ +     +DA+ 
Sbjct: 20  ALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEPVQFQDTMDALR 79

Query: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQA-RIGWWRYLSNTRQQEIAQFFIDKLQIAT 391
           +GI++  ++  +   +  +++ ENI L  +  + G+  +    RQ    Q  +DKL I  
Sbjct: 80  SGISMIHQELNL---VPHMTVAENIWLGREPMKYGFVDHRQLARQ---TQDLLDKLNIRL 133

Query: 392 PDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGM 451
             AD+ + +LS  +QQ V +A+ ++    ++++DEPT  +     A +  +IR L  +G 
Sbjct: 134 -SADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLRQQGK 192

Query: 452 SLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVM 493
           +++  S ++DE+ A ++++ V RD   V      E T Q ++
Sbjct: 193 AIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLI 234


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: 568
Number of extensions: 27
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 494
Length adjustment: 34
Effective length of query: 465
Effective length of database: 460
Effective search space:   213900
Effective search space used:   213900
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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