Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate RR42_RS10790 RR42_RS10790 ABC transporter permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Cup4G11:RR42_RS10790 Length = 501 Score = 116 bits (291), Expect = 9e-31 Identities = 66/186 (35%), Positives = 112/186 (60%), Gaps = 4/186 (2%) Query: 91 LTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLF 150 LT + LAL+L A + ++GVP+GI+ A+ R + + + + V+QT+PS L + L Sbjct: 303 LTCRHLALVLGAVGAASLLGVPLGIVAARRRRLGQVLMATVSVLQTVPSLALLAMLIPLL 362 Query: 151 G-LGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATP 209 G +G PA++A +YA+ P++R T G++QV A + EAA A G +PGQ+L VELPL+ P Sbjct: 363 GRIGVWPAMVALFLYALLPIVRNTLTGLQQVPAGMREAARALGFTPGQVLRYVELPLSMP 422 Query: 210 TIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDR 269 ++AG+ ++++ +A+ +GA G GE++ G+ D + I +LA++ Sbjct: 423 VLLAGIKTAAIISVGTATIAAFVGAGGYGERIATGLALNDHVLLMAGAIPAAVLALL--- 479 Query: 270 ITQGFG 275 + GFG Sbjct: 480 VQAGFG 485 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: 333 Number of extensions: 18 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: 501 Length adjustment: 30 Effective length of query: 255 Effective length of database: 471 Effective search space: 120105 Effective search space used: 120105 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