Align LacF, component of Lactose porter (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= TCDB::P29823 (298 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 147 bits (371), Expect = 3e-40 Identities = 94/271 (34%), Positives = 140/271 (51%), Gaps = 9/271 (3%) Query: 18 WLFVAPAIALISVFMLYPILRSLVLSLYT---GRGMMLKFSGTGNLVRLWNDPVFWQALQ 74 WL + PA+ I+ YP+LR+ LSL + F G N RLW D FW L Sbjct: 7 WLTI-PALLTITGVFAYPLLRAAWLSLQALNLNTQLQPVFIGLANYQRLWGDSRFWGDLF 65 Query: 75 NTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSMFSL 134 NT +F V V + + + L +A +L+ P R+ G RT+ LP V ++ + +F+ Sbjct: 66 NTTVFTVTSVSLELVLGLAIALLLHQPS-RWRGPLRTIALLPWVLPTAVMALGWAWIFND 124 Query: 135 D-GVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRSIY 193 GV N+ L +G I PI WL +P WA + ++ A W+ T + I LA Q I +Y Sbjct: 125 PYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPEDLY 184 Query: 194 EAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANSTLT 253 EA ++G +W F +T+P+L+P + + + LFD V T GGPANST T Sbjct: 185 EAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMT--GGGPANSTET 242 Query: 254 LSLYIYNLTFRFMPSFSYAATVSYVIVLMVA 284 L+LY Y R++ F Y AT++ V ++A Sbjct: 243 LALYAYTTALRYL-DFGYGATLAIVTAAILA 272 Lambda K H 0.329 0.141 0.435 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: 286 Number of extensions: 22 Number of successful extensions: 4 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: 298 Length of database: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 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: 48 (23.1 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