Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate PP_3559 PP_3559 glycine betaine ABC transporter (permease)
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Putida:PP_3559 Length = 282 Score = 300 bits (767), Expect = 3e-86 Identities = 152/275 (55%), Positives = 208/275 (75%) Query: 2 FPDSLNLSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMA 61 FP +L S +N + LV NYG +++S +L+ ++ +E +LR LPWWL++L Sbjct: 5 FPQTLQFSFADSINRLVDWLVLNYGDHLRSLSDQLLQLLVGLENLLRLLPWWLLLLLVGL 64 Query: 62 LACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSR 121 LA +SR + + ALL +G+LG+WD +QTLAL+L++T + V++GVP+GIL+A Sbjct: 65 LAWHASRSLLRSAVLVALLALIGMLGLWDKLLQTLALVLVSTGLCVLVGVPLGILLAARP 124 Query: 122 VVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVD 181 + R + LPVLDVMQT+P+FVYLIP LMLFGLGKVPA+ AT+IYA+PPL+RLT+LG+ Q+D Sbjct: 125 LARRLLLPVLDVMQTLPAFVYLIPVLMLFGLGKVPAVFATLIYALPPLVRLTELGLSQID 184 Query: 182 AEVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQV 241 +++AA G S Q L + LPLA P+IMAGLNQ++MMALSMVVVASMIGARGLGE V Sbjct: 185 PSLLQAAHGLGASRWQRLRRIALPLALPSIMAGLNQSVMMALSMVVVASMIGARGLGEDV 244 Query: 242 LNGIQTLDVGKGLEAGIGIVILAVVLDRITQGFGK 276 L GIQTL+VG+G+EAG+ IV LA+V+DRI+Q +G+ Sbjct: 245 LAGIQTLNVGQGMEAGLAIVALAMVIDRISQAYGR 279 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: 272 Number of extensions: 11 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: 282 Length adjustment: 26 Effective length of query: 259 Effective length of database: 256 Effective search space: 66304 Effective search space used: 66304 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 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