Align LacF, component of Lactose porter (characterized)
to candidate WP_106712771.1 CU102_RS19480 sugar ABC transporter permease
Query= TCDB::P29823 (298 letters) >NCBI__GCF_003010955.1:WP_106712771.1 Length = 307 Score = 140 bits (352), Expect = 5e-38 Identities = 89/274 (32%), Positives = 146/274 (53%), Gaps = 12/274 (4%) Query: 19 LFVAPAIALISVFMLYP---ILRSLVLSLYTGRGMMLKFSGTGNLVRLWNDPVFWQALQN 75 L +AP + ++ ++P + + V + + +F G+GN RL +D F AL+N Sbjct: 30 LMLAPTVLILLTLTIFPSVYMFYAAVHKISPNPDLPWEFVGSGNFARLLSDGQFHVALRN 89 Query: 76 TVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSMFSLD 135 T+IF V+ V + L LA +L+ +R +T++ +P + +A +I +K ++ Sbjct: 90 TIIFTVLAVTAEFLLGLGLALLLDK-YIRRLTFLKTVLMIPMMLPPIAVAITWKIIYEPQ 148 Query: 136 -GVVNNTLLAIGIIGEPI-GWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRSIY 193 GV+N + +G+ P+ W D A II+A W+WT + + LA L ++ Y Sbjct: 149 FGVLNEIMFRLGL---PLQAWAGDANLAMFSIIVADVWQWTPFIFLLMLAGLASLPVEPY 205 Query: 194 EAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANSTLT 253 EAA +DG SW +F LT+P LKPVI + + L+LFD V+ T GGPA+ T Sbjct: 206 EAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILT--GGGPADRTKV 263 Query: 254 LSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLS 287 LSLY+Y + +RF + YAA +S ++ +LS Sbjct: 264 LSLYVYQVAYRFADT-GYAAAISLFVLFATIILS 296 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: 271 Number of extensions: 18 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: 298 Length of database: 307 Length adjustment: 27 Effective length of query: 271 Effective length of database: 280 Effective search space: 75880 Effective search space used: 75880 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 24 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