Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 3608029 Dshi_1436 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Dino:3608029 Length = 513 Score = 203 bits (517), Expect = 6e-57 Identities = 117/274 (42%), Positives = 171/274 (62%), Gaps = 2/274 (0%) Query: 3 PDSLNLSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMAL 62 PD + L+ A V DFI V N F A++ I + +E IL PW +VI + + L Sbjct: 242 PD-IRLTGIAWVEDFIAWTVRNTEAFFDALTFGIRTLLDALEVILVQTPW-IVIASLIVL 299 Query: 63 ACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRV 122 + + A L +G+LG W+ M TLAL+ A +S+VIG+P+G+ A+ Sbjct: 300 LTWLTAGLRTAIYSSAFLAYMGLLGFWEAAMTTLALLGTAACLSIVIGIPLGMFAARRPR 359 Query: 123 VRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDA 182 P++D MQTMP+FV+++P + FG+GK A++ T+I+ P++RLT LG+R V Sbjct: 360 FYAFIQPIMDFMQTMPAFVFMVPVIAFFGVGKPAAVIVTMIFGGTPVVRLTVLGLRGVPE 419 Query: 183 EVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVL 242 V EAA +FG + +L V+LPLA P+I AG+NQTIM++L+MVVVAS+IGA+GLGE VL Sbjct: 420 SVREAAISFGANKWYLLTKVDLPLAGPSIRAGINQTIMLSLAMVVVASLIGAKGLGEDVL 479 Query: 243 NGIQTLDVGKGLEAGIGIVILAVVLDRITQGFGK 276 +Q +VG+G+ AG I+ A++LDRI QG K Sbjct: 480 EALQYANVGQGILAGFSILFCAMILDRIVQGARK 513 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: 405 Number of extensions: 15 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: 513 Length adjustment: 30 Effective length of query: 255 Effective length of database: 483 Effective search space: 123165 Effective search space used: 123165 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: 50 (23.9 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