GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Bb in Klebsiella michiganensis M5al

Align ABC-type Maltose/ Maltodextrin permease (characterized, see rationale)
to candidate BWI76_RS03240 BWI76_RS03240 maltodextrin ABC transporter permease

Query= uniprot:Q6MNM1
         (272 letters)



>FitnessBrowser__Koxy:BWI76_RS03240
          Length = 277

 Score =  193 bits (491), Expect = 3e-54
 Identities = 95/266 (35%), Positives = 170/266 (63%), Gaps = 5/266 (1%)

Query: 8   WISILLFSLFSIYPILYVLSVSLRP-DNAFQTQSLEIIGPNASFKNFVDLFATTDFLIWM 66
           ++ +LL +L  + P+++ +  SL+P +N F +   EI   + + +++ +L   T +L W 
Sbjct: 14  YLFLLLNALVVLGPVIWTVMSSLKPGNNLFSSGFTEI---SFTLEHYHNLLTGTPYLKWY 70

Query: 67  RNSLVVSAATTLLGVALASTSAYALARYRFRGRNMMLFSLLMTQMFPATMLMLPFYIILS 126
           +N+ +++    L+ + + + +A+  +RYRF+ +  +L S+L+ QMFPA + M   YI+LS
Sbjct: 71  KNTFILATCNMLISLVVVTITAFIFSRYRFKAKKKILMSILVLQMFPAFLSMTAIYILLS 130

Query: 127 KLRLIDSFWGLFLIYSSTALPFCIWQMKAYYDTIPRELEEAALLDGCSKWMIFYKIILPV 186
           K+ LID++ GL L+Y + +LPF  W +K Y+D IP  L+EAA +DG     IF++IILP+
Sbjct: 131 KMNLIDTYIGLLLVYVTGSLPFMTWLVKGYFDAIPTSLDEAAKIDGAGHLTIFFEIILPL 190

Query: 187 SSPALVITALFSFMSSWSEYVIAAVVLQDPQLYTLPLGLRSF-QASLATQWGLYAAGALI 245
           + P LV  AL SF   W ++++  ++L+     TL +G+ S+  ++ A  + L+AAGAL+
Sbjct: 191 AKPILVFVALVSFTGPWMDFILPTLILRSEDKMTLAIGIFSWISSNSAENFTLFAAGALL 250

Query: 246 VSVPVLILFISISRYLVSGLTMGSVK 271
           V+VP+ +LFI   +++ +GL  G+VK
Sbjct: 251 VAVPITLLFIVTQKHITTGLVSGAVK 276


Lambda     K      H
   0.329    0.139    0.421 

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: 214
Number of extensions: 14
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: 272
Length of database: 277
Length adjustment: 25
Effective length of query: 247
Effective length of database: 252
Effective search space:    62244
Effective search space used:    62244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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