Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate BPHYT_RS25070 BPHYT_RS25070 choline ABC transporter permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__BFirm:BPHYT_RS25070 Length = 300 Score = 248 bits (634), Expect = 9e-71 Identities = 132/270 (48%), Positives = 186/270 (68%), Gaps = 3/270 (1%) Query: 8 LSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALAC-RS 66 + + A V+ + L+ + F +I VI IE L+ +P W ++ F+ + R Sbjct: 5 IPLGAWVDHGVHYLLDHDAKTFDSIGKVIESFAAVIEHGLQAVPMWALMAFFVGIGLWRV 64 Query: 67 SRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNI 126 R++L + LL + G WD + TL L L +T++S+++GVP+GI AKSR V I Sbjct: 65 GWRFALFTLLAMLL--IYGTGFWDQMVITLGLTLSSTLISLLLGVPLGIWTAKSRTVEMI 122 Query: 127 TLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVE 186 PVLD+MQTMP+FVYLIPA MLFGLG+VP IL+T+I+A+PP +RLT LGI+ V+ E+VE Sbjct: 123 VRPVLDLMQTMPAFVYLIPAAMLFGLGRVPGILSTVIFAMPPAVRLTSLGIKHVNREIVE 182 Query: 187 AATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQ 246 A AFG +P Q+L+ V+ P A P+IM G+NQTIMMALSMV++ASM+GA GLG VL IQ Sbjct: 183 AGQAFGCTPLQLLYKVQFPNALPSIMTGVNQTIMMALSMVIIASMVGAGGLGNDVLASIQ 242 Query: 247 TLDVGKGLEAGIGIVILAVVLDRITQGFGK 276 LD+G G E+G+ +V+LA++LDRIT+ FG+ Sbjct: 243 RLDIGLGFESGLSVVMLAIILDRITESFGR 272 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: 279 Number of extensions: 15 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: 300 Length adjustment: 26 Effective length of query: 259 Effective length of database: 274 Effective search space: 70966 Effective search space used: 70966 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