Align ABC transporter for L-Fucose, permease component 2 (characterized)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein
Query= reanno::Smeli:SM_b21105 (288 letters) >FitnessBrowser__Koxy:BWI76_RS06705 Length = 283 Score = 147 bits (370), Expect = 3e-40 Identities = 87/276 (31%), Positives = 153/276 (55%), Gaps = 8/276 (2%) Query: 14 LKVAHLAGLFLAMLVICLPGLWIVLSSLRPTVEIMAKPPVWIPETLSLDAYRAMFSGAGQ 73 L + L +F++ ++I P +W V +SL +++ IPE LS Y +F+G Sbjct: 15 LSLTWLVVIFVSTMII-YPLVWTVGASLNAGNSLLSTSI--IPENLSFQHYADLFNG--- 68 Query: 74 GGVPVWDYFRNSLIVSVTSTVIALAIGLSGGYAFARYRFKAKSAIFLGFMLTRAVPGIAL 133 V ++ NS+ +S + V+ L YAF+R+RFK + + F+L + +P + Sbjct: 69 -NVNYLTWYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQMIPQFSA 127 Query: 134 SLPLFMLYARTGIIDTHFSLILTYVALNVPFTIWLIDGFFRQVPKDLAEAAQIDGCTPWQ 193 + +F+L G+I++H +L+L YV +P WL+ G+ +PKDL E+A++DG + ++ Sbjct: 128 LIAIFVLSQLLGLINSHLALVLIYVGGMIPMNTWLMKGYLDAIPKDLDESARMDGASSFR 187 Query: 194 AFWQVEFPLAGPGIASAGIFAFLTSWNEYALASQITRSVNSKTLPVGLLDYTAE-FTIDW 252 F+++ PL+ P +A +F+F ++ L+S I R+ + TLP+GL + A+ + Sbjct: 188 IFFEIIMPLSKPILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVAQKMGASY 247 Query: 253 RGMCALAVVMIVPALTLTFIIQKHLVSGLTFGAVKG 288 A AV++ VP L +QK+ VSGLT G+ KG Sbjct: 248 TTYAAGAVLIAVPVAILYLALQKYFVSGLTSGSTKG 283 Lambda K H 0.328 0.141 0.442 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: 228 Number of extensions: 13 Number of successful extensions: 3 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: 288 Length of database: 283 Length adjustment: 26 Effective length of query: 262 Effective length of database: 257 Effective search space: 67334 Effective search space used: 67334 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 (21.8 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