Align LacF, component of Lactose porter (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= TCDB::P29823 (298 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 114 bits (285), Expect = 3e-30 Identities = 78/250 (31%), Positives = 134/250 (53%), Gaps = 9/250 (3%) Query: 18 WLFVAPAIALISVFMLYPILRSLVLSLYTGRGMML--KFSGTGNLVRLWNDPVFWQALQN 75 WL ++P++ + +F +P+ RS+ SL+ R + ++ G N RL+ D VFWQ+L N Sbjct: 8 WLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFADSVFWQSLVN 67 Query: 76 TVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSSLVAYSILFKSMFSLD 135 +++ ++ V +T+AL+LA L R + RT F P + +V+ + L+ +F Sbjct: 68 NLLYILLTVVPGVTLALLLAVALTENH-RVNRWLRTAFFFPMIIPMVSAAALWLFIFMPG 126 Query: 136 -GVVNNTLLAI-GIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMIFYLAALQNIDRSIY 193 G++++ L + G + WL A + + + W++ GY M+F+LA LQ+I S Sbjct: 127 LGLLDHYLAKLFGPMNN--NWLGRSNSALLALALIGVWKFAGYYMLFFLAGLQSIPASTR 184 Query: 194 EAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTLQLFDEVYNFTEGTGGPANSTLT 253 EAA ++G F +T+P+L+P + F T+ I ++ D V T GGP N+T Sbjct: 185 EAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVAVMTR--GGPDNATTV 242 Query: 254 LSLYIYNLTF 263 L YI NL + Sbjct: 243 LLYYIQNLAW 252 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: 261 Number of extensions: 23 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: 290 Length adjustment: 26 Effective length of query: 272 Effective length of database: 264 Effective search space: 71808 Effective search space used: 71808 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