GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Klebsiella michiganensis M5al

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate BWI76_RS23390 BWI76_RS23390 oligogalacturonide ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__Koxy:BWI76_RS23390
          Length = 375

 Score =  317 bits (811), Expect = 4e-91
 Identities = 180/375 (48%), Positives = 241/375 (64%), Gaps = 22/375 (5%)

Query: 1   MAPVTLKKLVKRYG-ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59
           MA V   KL K Y    + VHGIDL++ D EF+ +VGPSGC KSTTLRM+AGLE +SGG 
Sbjct: 1   MAEVIFNKLEKVYSNGFKAVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGGE 60

Query: 60  IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119
           + IG + VN+L P+AR I+MVFQ+YALYPHMTV EN+ F LK++  P ++I+ +V EAA 
Sbjct: 61  VRIGEKIVNNLAPKARGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQIEAQVNEAAK 120

Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179
           IL+L  LL+R P QLSGGQ QRVA+GRAIV++PDVFLFDEPLSNLDAKLR  +R  I  L
Sbjct: 121 ILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISDL 180

Query: 180 HARMQ-----ATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234
           H +++     AT +YVTHDQ EAMT+ DRI +M+ GHI QV TP++++ +P   FVAGFI
Sbjct: 181 HKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHKPKNMFVAGFI 240

Query: 235 GSPPMNMEEAVLTD--GKLAFASG-ATLPLPPRFRSLV--REGQKVTFGLRPDDVYPSGH 289
           G+P MN+  + L +  G+L    G   LPL  R +S V   + Q+V FG+RP+ V  S  
Sbjct: 241 GAPEMNIRPSQLVEQAGRLHLTVGDGLLPLNDRLQSKVDTHKNQQVFFGVRPEFVSISDE 300

Query: 290 GLHAGDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRP---LRPG--EAVP 344
               G           +   E +G+E  V+ +    +  +R+ +      +  G    V 
Sbjct: 301 PFAEGSCTG------EMVRVENMGHEFFVYLKVADYELTARVPSDEAKPMIEKGLHRKVH 354

Query: 345 MSFDLARAHLFDGET 359
             FDL + H+FD +T
Sbjct: 355 FKFDLNKCHIFDAKT 369


Lambda     K      H
   0.320    0.137    0.397 

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: 369
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: 365
Length of database: 375
Length adjustment: 30
Effective length of query: 335
Effective length of database: 345
Effective search space:   115575
Effective search space used:   115575
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: 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