GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Pseudomonas litoralis 2SM5

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein

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



>NCBI__GCF_900105005.1:WP_090274680.1
          Length = 378

 Score =  213 bits (542), Expect = 7e-60
 Identities = 130/342 (38%), Positives = 189/342 (55%), Gaps = 8/342 (2%)

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

Query: 64  DRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQI 123
            +N+T   P  R I M+FQSYAL+P MTVE+N++FGLK  K+   EI +RV    +++ +
Sbjct: 81  GQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVHM 140

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

Query: 184 KNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFR 243
             T I VTHDQ EA+T+A RIA+M  G I Q+  PM IY +P N  VA F+G  S+N F 
Sbjct: 201 GVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVG--SVNIFE 258

Query: 244 GE-VEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEP---T 299
           GE V   D    +    +   +      T     +  +  LRPE V V   +  +P    
Sbjct: 259 GEIVADMDDHVIIECPQLDRQIYLGHGVTTRAEDKSAIYALRPEKVFVTTEQPEQPYNWA 318

Query: 300 HQAVVDIEEPMGADNLLWLTF-AGQSMSVRIAGQRRYPPGST 340
           H  V DI   +G  ++ ++   +G+ +    A   R  P  T
Sbjct: 319 HGEVHDIAY-LGGHSVYYIKLDSGKMVQAFFANSERRLPRPT 359


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: 333
Number of extensions: 12
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 24 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