GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Escherichia coli BW25113

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 16768 b2678 glycine betaine transporter subunit (NCBI)

Query= TCDB::Q9KKE2
         (285 letters)



>FitnessBrowser__Keio:16768
          Length = 354

 Score =  238 bits (608), Expect = 1e-67
 Identities = 126/263 (47%), Positives = 180/263 (68%), Gaps = 1/263 (0%)

Query: 14  VNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALACRSSRRWSLT 73
           V + I  +VT++  VF+ +   +   +   + +L G+P  + I+ F  +A + S    + 
Sbjct: 68  VTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQISGV-GMG 126

Query: 74  LAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDV 133
           +A    L  +G +G W   M TLAL+L A +  +VIG+P+GI +A+S     I  P+LD 
Sbjct: 127 VATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIRPLLDA 186

Query: 134 MQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193
           MQT P+FVYL+P +MLFG+G VP ++ TII+A+PP+IRLT LGI QV A+++EA+ +FG 
Sbjct: 187 MQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEASRSFGA 246

Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253
           SP Q+LF V+LPLA PTIMAG+NQT+M+ALSMVV+ASMI   GLG+ VL GI  LD+G  
Sbjct: 247 SPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRLDMGLA 306

Query: 254 LEAGIGIVILAVVLDRITQGFGK 276
              G+GIVILA++LDR+TQ  G+
Sbjct: 307 TVGGVGIVILAIILDRLTQAVGR 329


Lambda     K      H
   0.327    0.142    0.422 

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: 366
Number of extensions: 26
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: 285
Length of database: 354
Length adjustment: 27
Effective length of query: 258
Effective length of database: 327
Effective search space:    84366
Effective search space used:    84366
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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