Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc02379 SMc02379 permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Smeli:SMc02379 Length = 295 Score = 244 bits (623), Expect = 2e-69 Identities = 119/263 (45%), Positives = 180/263 (68%) Query: 14 VNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALACRSSRRWSLT 73 +++ ++ YG ++ + ++ E + PW ++++ +A +SR W + Sbjct: 22 IDEGFRSFTRAYGDAIESFFDPLQFFLIHAERFMTRTPWPIILILIAVIAWFASRNWKIV 81 Query: 74 LAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDV 133 L +G L +WD TM+T++++ + T++S+ IG+PMGI++++S +NI PVLDV Sbjct: 82 AGAIGTLLLIGYLDMWDDTMKTISMIFVCTVLSIAIGIPMGIIMSRSDRFQNIVNPVLDV 141 Query: 134 MQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193 MQTMPSFVYLIP +ML G+GKVP ++A +IYA+PP+IRLT+LGIR VD +V+EAA AFG Sbjct: 142 MQTMPSFVYLIPVVMLLGIGKVPGLIAVVIYAIPPMIRLTNLGIRLVDKDVLEAADAFGS 201 Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253 S Q L V++PLA PTIMAG+NQTIMMAL+MVV+ASMIG +GLG+ VL I G Sbjct: 202 SNWQKLKNVQMPLALPTIMAGINQTIMMALAMVVIASMIGVQGLGQPVLKAIANQYFTLG 261 Query: 254 LEAGIGIVILAVVLDRITQGFGK 276 + G+ IV +A++ DR++Q +G+ Sbjct: 262 IFNGLAIVGIAIIFDRVSQAYGR 284 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: 251 Number of extensions: 6 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: 295 Length adjustment: 26 Effective length of query: 259 Effective length of database: 269 Effective search space: 69671 Effective search space used: 69671 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