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.
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:
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