GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cebF in Klebsiella michiganensis M5al

Align CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease

Query= TCDB::Q9X9R6
         (306 letters)



>FitnessBrowser__Koxy:BWI76_RS03135
          Length = 290

 Score =  117 bits (294), Expect = 2e-31
 Identities = 79/285 (27%), Positives = 140/285 (49%), Gaps = 9/285 (3%)

Query: 19  PYAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNAL 78
           P+  ++P  L    F+  PL  + + SL + ++ + D   + GL+N+  L +   FW +L
Sbjct: 7   PWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVS-DGGQYVGLENFSRLFADSVFWQSL 65

Query: 79  KNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSW 138
            N L   +++ VP +  AL LA  L    R +   R     P    + +A  ++  ++  
Sbjct: 66  VNNLLYILLTVVPGVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVSAAALWLFIFMP 125

Query: 139 DGGMVN-WILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYE 197
             G+++ ++   FG    NW      +  A++ I +W++ GY  L +LA +Q+IPA   E
Sbjct: 126 GLGLLDHYLAKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSIPASTRE 185

Query: 198 SAALDGANRWQQFRHVTVPQLRPTILFTVVVSTI-GATQLFGEPLLFGGVSGSKGGSEHQ 256
           +A ++GA R Q F  VT+P LRPT+ F +  + I   TQ+    ++      ++GG ++ 
Sbjct: 186 AAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVM------TRGGPDNA 239

Query: 257 YQTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIVAAVNLLLTRR 301
              L  Y+ +  W   +LGKASA  +     L   + +NL L  +
Sbjct: 240 TTVLLYYIQNLAWDTHDLGKASAATFLTLAGLFAFSLINLKLLEK 284


Lambda     K      H
   0.324    0.137    0.441 

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: 265
Number of extensions: 15
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: 306
Length of database: 290
Length adjustment: 26
Effective length of query: 280
Effective length of database: 264
Effective search space:    73920
Effective search space used:    73920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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