Align D-lactate transporter, permease component 2 (characterized)
to candidate Ac3H11_68 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_68 Length = 328 Score = 140 bits (354), Expect = 3e-38 Identities = 99/322 (30%), Positives = 156/322 (48%), Gaps = 39/322 (12%) Query: 11 GLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKD 70 GL G +IA GLTL+FG + V+NF HG +GAF A +V + D TQ Sbjct: 39 GLAMGMIIFIIASGLTLVFGLMDVLNFGHGVFIALGAFVATSVLGAMG------DYTQSA 92 Query: 71 FLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRP 130 L L P A+L A+ + VG ER +++ Y + Sbjct: 93 DLWRNLMAVLP---------------------AMLVAMAVAGAVGLAFERFIVRPVYGQ- 130 Query: 131 HADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRVVYF 190 H QIL+T G I+ +E +K +G I P P+ + G + +G D +R++ Sbjct: 131 HLKQILITMGGMIIGEEFIKVIWGPQQIPLPLPEGMRGSLLVG-----DAAIEKYRLLAM 185 Query: 191 FFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGV 250 +++ G + L T G+++RAG+ DRE V LG I R F +F + +A+AGL GV Sbjct: 186 AVGLLVFGVLAWTLSRTKVGLLIRAGVQDREMVESLGYRIRRLFIGVFVVGSALAGLGGV 245 Query: 251 MYTPI-NSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIP 309 M+ S MG VL F+V+++GG+GS GA++ L+G++ ++ L+P Sbjct: 246 MWGLYQQSVVPQMGAQVNVLIFIVIIIGGLGSTGGALIGALLVGLMANYTGF-----LVP 300 Query: 310 GIDQIIIYVVAIIILLTRPRGL 331 + + + ILL RP+G+ Sbjct: 301 KVALFSNITLMVAILLWRPQGV 322 Lambda K H 0.329 0.147 0.439 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: 272 Number of extensions: 19 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: 340 Length of database: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 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: 49 (23.5 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