Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_005814528.1 DHAF_RS11460 ABC transporter permease
Query= TCDB::Q9KKE2 (285 letters) >NCBI__GCF_000021925.1:WP_005814528.1 Length = 279 Score = 247 bits (631), Expect = 2e-70 Identities = 129/260 (49%), Positives = 182/260 (70%), Gaps = 1/260 (0%) Query: 14 VNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALACRSSRRWSLT 73 VN + L+ +G F A + + + L +PW++++L F ALA R+ + W L Sbjct: 10 VNQGVDTLLFYFGSAFDAFTDSVTSMTDAMREGLDVVPWFILVLLFAALAWRA-KGWRLA 68 Query: 74 LAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDV 133 L L + L +W + TL L+L+A++VS+VIG+P+GIL A+ + P+LD Sbjct: 69 LGTTVGLCLIYNLELWPAFLDTLILVLLASLVSLVIGIPLGILGARHNGFHRVLSPILDF 128 Query: 134 MQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193 MQTMPSFVYLIPALM F LG V AI AT+I+A+PP+IRLT LGIRQV A++VE AFG Sbjct: 129 MQTMPSFVYLIPALMFFSLGTVSAIFATVIFAMPPVIRLTALGIRQVPADLVEVGEAFGS 188 Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253 + Q+L+ ++LPLA PTIMAG+NQT+M++LSMVV+++MIGA+GLG VL GI +D+GKG Sbjct: 189 NSRQMLWKIQLPLALPTIMAGINQTMMLSLSMVVISAMIGAQGLGAGVLAGISGMDIGKG 248 Query: 254 LEAGIGIVILAVVLDRITQG 273 E G+ +VILA++LDR++QG Sbjct: 249 FEYGLAVVILAMILDRLSQG 268 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: 277 Number of extensions: 14 Number of successful extensions: 2 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: 279 Length adjustment: 26 Effective length of query: 259 Effective length of database: 253 Effective search space: 65527 Effective search space used: 65527 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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