GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Shewanella loihica PV-4

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 5210054 Shew_2501 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q9WXN4
         (268 letters)



>FitnessBrowser__PV4:5210054
          Length = 337

 Score =  119 bits (299), Expect = 7e-32
 Identities = 75/245 (30%), Positives = 137/245 (55%), Gaps = 8/245 (3%)

Query: 22  RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT----SGEIYFEGKDIWKD 77
           R++A++ VS  +   E+  LVGESGSG+T  AK IL +        +  + ++G+++  D
Sbjct: 19  RVKALERVSLTLNPGEVHGLVGESGSGRTLLAKAILGIPGHNWTIQADRMMWDGQNLM-D 77

Query: 78  IKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKK--EALELIKE 135
           +   E  V    ++  +FQDP +S +P   V   + +A+   +  P  K+  +  +  ++
Sbjct: 78  MSPSERRVLMGSEMAMIFQDPISSLDPAIAVGTQIIEAMPENKELPWWKRGSDKRKKAQQ 137

Query: 136 SLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194
            L +VGI + + ++  Y  ++S G+ Q++MIA     +P L++ADEPT+ ++  ++  I 
Sbjct: 138 WLHKVGIKETQKIMSSYAWELSDGECQKVMIAIAVANQPRLLIADEPTNSMEVRTQAQIF 197

Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254
           +LL +L + Q  SI+ I+H+L       D + VM +G+++E G    V+  P H YTK L
Sbjct: 198 RLLSKLNQLQNVSILLISHELETLSQWCDRLTVMYSGQVMESGVTSDVIANPYHPYTKAL 257

Query: 255 VGSIP 259
           + +IP
Sbjct: 258 LDNIP 262


Lambda     K      H
   0.319    0.139    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: 196
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: 268
Length of database: 337
Length adjustment: 27
Effective length of query: 241
Effective length of database: 310
Effective search space:    74710
Effective search space used:    74710
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 (21.7 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