GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Shewanella oneidensis MR-1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  211 bits (536), Expect = 3e-59
 Identities = 120/297 (40%), Positives = 183/297 (61%), Gaps = 6/297 (2%)

Query: 4   VSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIK 63
           + +  +S  F  V  +D ++L I+ GE   LLG SG GKSTLL  +AG    + G+I++ 
Sbjct: 21  LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLD 80

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
             ++T   P +R I M+FQSYAL+P MTV +N++FGLK  K+P AEIE+RV+   +++ +
Sbjct: 81  GEDITDLPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHM 140

Query: 124 QPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSL 183
           +   KRKP +LSGGQRQRVA+ R+L +   + L DEP+  LD KLR+++++E+  + + +
Sbjct: 141 EQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERV 200

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243
             T + VTHDQ EA+T+A RI++M  G I Q   PM IY +P +  +A FIG  S+N F 
Sbjct: 201 GVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIG--SVNLFS 258

Query: 244 GEVEPKD-GRSFVRAGGIAFD-VTAYPAHTRLQPGQKVVLGLRPEHVKVD-EARDGE 297
           GE+E  +     ++   +A      Y   T L+  ++V L +RPE   +  E  +GE
Sbjct: 259 GEIEVDEVDHLIIKPNDLARSFYVGYGVTTSLE-DKRVWLAVRPEKTIISREQPEGE 314


Lambda     K      H
   0.320    0.137    0.392 

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: 330
Number of extensions: 13
Number of successful extensions: 1
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: 361
Length of database: 378
Length adjustment: 30
Effective length of query: 331
Effective length of database: 348
Effective search space:   115188
Effective search space used:   115188
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