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_RS17840 BWI76_RS17840 sugar ABC transporter permease

Query= uniprot:A3DHA3
         (284 letters)



>FitnessBrowser__Koxy:BWI76_RS17840
          Length = 313

 Score =  148 bits (373), Expect = 2e-40
 Identities = 94/287 (32%), Positives = 146/287 (50%), Gaps = 6/287 (2%)

Query: 2   RHKEALAGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRGVGSF--EFAGLDNFKSVIASNS 59
           + K AL  +LF +P L  F  F  IP    +   F +   +   E+ GLDNF    A   
Sbjct: 26  KRKRALIPWLFLAPALIIFSWFKFIPMIQGLVMSFYKVNFNQPNEWVGLDNFTRAFADAE 85

Query: 60  YRLAVKNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQ 119
              AV NTL++  V++    I++  LAMLL    R  R+ R    LP V   A +  +W+
Sbjct: 86  LHAAVVNTLLYVVVTMFAAAILAFFLAMLLEGPARHLRFIRTAIFLPAVTSAAIVAEMWR 145

Query: 120 ITFNEF--GVLNNLLNHFGIAGVEWL-NSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIP 176
           I FN    GV+N++L+ FG+A   +L +S  ++ V++LL++WK   YN+++F AGL  I 
Sbjct: 146 ILFNPTPNGVVNHILSWFGVADQGFLASSDQALGVIMLLHIWKAVPYNMVIFIAGLAGIS 205

Query: 177 KDYYDAASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNYPP-LN 235
           +D YDAA++DGA  +     +TLP ++P +  V ++S I  F+VF E Y   G  P    
Sbjct: 206 RDLYDAANVDGASWWNRLRYVTLPGMIPALSVVLMLSFIRGFRVFAEVYATTGGGPSNAT 265

Query: 236 MYMLQHFMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYKIEGRYGK 282
             ++ H     F   +Y   S  S L+  F V +      ++ R  +
Sbjct: 266 EMVMTHIYKLGFEQFDYGYASAVSFLLFTFTVLLTICHLTLKKRIAR 312


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: 220
Number of extensions: 9
Number of successful extensions: 3
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: 313
Length adjustment: 27
Effective length of query: 257
Effective length of database: 286
Effective search space:    73502
Effective search space used:    73502
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: 48 (23.1 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