GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Escherichia coli BW25113

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 17602 b3541 dipeptide transporter (NCBI)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Keio:17602
          Length = 327

 Score =  232 bits (592), Expect = 8e-66
 Identities = 131/316 (41%), Positives = 187/316 (59%), Gaps = 9/316 (2%)

Query: 13  LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGG 72
           LL    L  +F       +AVD IS  +K+GE +G+VGESG GKS     I+ L+   G 
Sbjct: 3   LLNVDKLSVHFGDESAPFRAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGLIDYPGR 62

Query: 73  ----KIFFEGKDITNLNDKEMKPY-RKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127
               K+ F G+D+  +++KE +     ++ +IFQDP+ SLNP  TVG  I + + +H+ G
Sbjct: 63  VMAEKLEFNGQDLQRISEKERRNLVGAEVAMIFQDPMTSLNPCYTVGFQIMEAIKVHQGG 122

Query: 128 TKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185
            K  RR+R  +LL+ VGI      ++ +PH+ SGG  QR+ IA A+A  PK ++ DEP +
Sbjct: 123 NKSTRRQRAIDLLNQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPTT 182

Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245
           ALDV+IQAQII+LL E+QQK  ++ + I H+LA+V   +HK+ VMY G++VE GD   IF
Sbjct: 183 ALDVTIQAQIIELLLELQQKENMALVLITHDLALVAEAAHKIIVMYAGQVVETGDAHAIF 242

Query: 246 LNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEK 305
             P HPYT+ALL+++P+   D  K+R  SL G +P   D P GC    RC      C  +
Sbjct: 243 HAPRHPYTQALLRALPEFAQD--KERLASLPGVVPGKYDRPNGCLLNPRCPYATDRCRAE 300

Query: 306 EPELTEVEKNHFVSCH 321
           EP L  +       CH
Sbjct: 301 EPALNMLADGRQSKCH 316


Lambda     K      H
   0.321    0.142    0.417 

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: 301
Number of extensions: 11
Number of successful extensions: 4
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: 328
Length of database: 327
Length adjustment: 28
Effective length of query: 300
Effective length of database: 299
Effective search space:    89700
Effective search space used:    89700
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: 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