GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdC1 in Klebsiella michiganensis M5al

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= uniprot:A3DHA3
         (284 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score =  108 bits (271), Expect = 1e-28
 Identities = 84/280 (30%), Positives = 139/280 (49%), Gaps = 9/280 (3%)

Query: 10  YLFSSPYLAGFLIFFAIPSAMSVYYCF--TRGVGSF-EFAGLDNFKSVIASNSYRLAVKN 66
           +L  SP L   L+F   P   SVY     TR V    ++ GL+NF  + A + +  ++ N
Sbjct: 8   WLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLVN 67

Query: 67  TLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQITFNE-F 125
            L++  ++V   + ++LLLA+ L +  R  R+ R  F  P++IP+ S   +W   F    
Sbjct: 68  NLLYILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWLFIFMPGL 127

Query: 126 GVLNNLLNH-FGIAGVEWLN-SKWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYDAA 183
           G+L++ L   FG     WL  S  ++  L L+ VWK  GY ++ F AGL SIP    +AA
Sbjct: 128 GLLDHYLAKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSIPASTREAA 187

Query: 184 SIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNYPPLNMYMLQHFM 243
            ++GA   + F  +TLPLL PT+ FV   ++I S        ++    P     +L +++
Sbjct: 188 IMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTRGGPDNATTVLLYYI 247

Query: 244 NN---NFNNLNYQRLSTASLLMELFIVAIVFLMYKIEGRY 280
            N   + ++L     +T   L  LF  +++ L    +G +
Sbjct: 248 QNLAWDTHDLGKASAATFLTLAGLFAFSLINLKLLEKGAH 287


Lambda     K      H
   0.331    0.144    0.444 

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: 223
Number of extensions: 11
Number of successful extensions: 2
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: 284
Length of database: 290
Length adjustment: 26
Effective length of query: 258
Effective length of database: 264
Effective search space:    68112
Effective search space used:    68112
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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