GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Klebsiella michiganensis M5al

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate BWI76_RS17830 BWI76_RS17830 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Koxy:BWI76_RS17830
          Length = 364

 Score =  311 bits (796), Expect = 2e-89
 Identities = 182/380 (47%), Positives = 245/380 (64%), Gaps = 26/380 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M ++ L+++ K Y +A  + +++ +L I D EF V VGPSGCGKST LRMIAGLE+I+ G
Sbjct: 1   MGSVVLNSVRKSYGDA--HVIKDVSLTIPDGEFCVLVGPSGCGKSTLLRMIAGLEEISGG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            ++I+++ + +  PK RDIAMVFQ+YALYP M+V ENM F LK+ K  K +IN++V+EAA
Sbjct: 59  EVHINERNVTEVEPKLRDIAMVFQSYALYPQMTVRENMGFALKMAKLPKAEINQKVNEAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            +LGL   LER P DLSGGQRQRVAMGRAIVR  +VFL DEPLSNLDAKLR  +R EI +
Sbjct: 119 ALLGLEPLLERLPKDLSGGQRQRVAMGRAIVRKPQVFLFDEPLSNLDAKLRTQVRGEIRE 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +HRR+  T++YVTHDQ EAMT+   IV++            GRIEQ GTP ELY+ PAN 
Sbjct: 179 LHRRLKTTSVYVTHDQIEAMTMGQMIVVLRD----------GRIEQAGTPLELYDRPANL 228

Query: 241 FVAGFIGSPAMNFFEVTV----EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296
           FVAGFIGSP +N     V        L  +DG  LALP G  ++ +     G++V   IR
Sbjct: 229 FVAGFIGSPEINQLPGEVVLNGNATSLRLKDGSLLALPAGL-RVTD-----GQQVVYAIR 282

Query: 297 PEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKV 356
           PE ++   +VHE   +A + A +   E  GS+  L+   G   FT+    R +   G+K+
Sbjct: 283 PEQVN---VVHEARDDA-LAAKVTAVENTGSDMQLFCDTGGGAFTSVFKQRLAVKEGDKI 338

Query: 357 QLTFNIAKGHFFDLETEKRI 376
            L   ++  H FD ++ +RI
Sbjct: 339 WLQPKLSGVHLFDAQSGQRI 358


Lambda     K      H
   0.318    0.135    0.379 

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: 356
Number of extensions: 17
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: 377
Length of database: 364
Length adjustment: 30
Effective length of query: 347
Effective length of database: 334
Effective search space:   115898
Effective search space used:   115898
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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