Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate GFF4157 HP15_4097 inner-membrane translocator
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Marino:GFF4157 Length = 347 Score = 165 bits (417), Expect = 3e-45 Identities = 107/317 (33%), Positives = 160/317 (50%), Gaps = 27/317 (8%) Query: 127 KLSQAERDKRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLG 186 ++ A++ D Q WLG +++ L FPF + D LL +G L+ ++ Sbjct: 2 RIGDAKQSYEADEAIWTSQTQKLWLG-FFLLILLVFPF--VVDSYLLYLGCLVGIAVIST 58 Query: 187 WGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFP 246 GLNI+ G GL+ LG F VGAY+ A L+ F V L LAG +AA G+L+G P Sbjct: 59 TGLNILTGFTGLISLGQAGFMGVGAYTVAWLSINTALPFPVTLVLAGLMAAAVGILVGLP 118 Query: 247 VLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTA 306 LR++G Y AI TL + I W TGG G+S P Sbjct: 119 SLRVKGLYLAIATLAASVFLHFIFAEWESVTGGMGGLSLEPA------------------ 160 Query: 307 AFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLG 366 +FGL F +Y++I+ LA+++ L V + +GRA+ A+R+ DI+ LG Sbjct: 161 ---HLFGLTF---QSDFMMYFIIVPLAVLMVLAARNVFRTRIGRAFIAIRDRDISAEILG 214 Query: 367 INRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGV 426 IN KL +FA+++ + G AG FA ++PESF S LA V++GGMG+ +G Sbjct: 215 INLLRYKLMSFALSSFYAGIAGGLFAYFYRVVTPESFPLSMSIFYLAAVIVGGMGNLLGG 274 Query: 427 VVAAFLVIGLPEAFREL 443 ++ A + +PEA + L Sbjct: 275 ILGAAFMTLVPEALKLL 291 Lambda K H 0.329 0.144 0.438 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: 474 Number of extensions: 43 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 505 Length of database: 347 Length adjustment: 32 Effective length of query: 473 Effective length of database: 315 Effective search space: 148995 Effective search space used: 148995 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: 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