Align D-lactate transporter, permease component 2 (characterized)
to candidate WP_011383887.1 AMB_RS07460 ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >NCBI__GCF_000009985.1:WP_011383887.1 Length = 618 Score = 166 bits (421), Expect = 1e-45 Identities = 104/335 (31%), Positives = 170/335 (50%), Gaps = 47/335 (14%) Query: 1 MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60 M +Q LNGL S+ L+A GL++IFG +VNFAHG+ +M+GA+ A T+ + LS Sbjct: 1 MSFFFIQFLNGLASASSLFLVASGLSIIFGVSRIVNFAHGSFYMLGAYMAFTLVQKLS-- 58 Query: 61 FETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIID-WAVPLAILFAIPIMIGVGYVME 119 GG + W AI+ A + VG V+E Sbjct: 59 -------------------------------GGTVFGFWG---AIVLAAAAVALVGAVVE 84 Query: 120 RGLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMD 179 L++ Y+ P Q+L TFGL +++Q++V +G + P L G ++ I G Sbjct: 85 MVLLRRIYQAPELLQLLATFGLVLIVQDLVLVLWGPEDLLGPRAPGLKGAID---IFGQS 141 Query: 180 IVYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFG 239 +P + V V++G ++ T +G ++RA DRE V LG+N FT +F Sbjct: 142 --FPQYDFVLIILGPVVLGLLWLLFHRTRWGTLIRAATQDREMVAALGVNQAWLFTSVFT 199 Query: 240 IAAAVAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFA 299 + A +AGL G + P + N+ M + + +FV+VV+GG+GS+ GA LA ++G L +F Sbjct: 200 LGAFLAGLGGAVQLPREAVNHVMDLQIITEAFVIVVIGGLGSVLGAFLAAVIIGELNAFG 259 Query: 300 SMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMGR 334 + + P + ++ ++V +IL+ RP GL+G+ Sbjct: 260 IL-----IFPQLTLVLTFLVMAVILVVRPWGLLGK 289 Score = 45.4 bits (106), Expect = 4e-09 Identities = 69/322 (21%), Positives = 119/322 (36%), Gaps = 68/322 (21%) Query: 18 YALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKDFLGNPLK 77 +AL A L + GT G+V+F H A F +G++ A + + + T G L Sbjct: 343 FALFAASLHFMMGTGGMVSFGHAAYFGLGSYGAALMVKYFGIPMLAALVT-----GPLLA 397 Query: 78 VKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRPHADQILV 137 V WF + GA + L + FA Sbjct: 398 AAAALVFGWFCVRLAGAYL---AMLTLAFA------------------------------ 424 Query: 138 TFGLAIVLQEVVKYFYGANPIQT--PAPDALNGVVNLGSIIGMDIVYPVWRVVYFFFAVV 195 A+V Q + G N + PAP A N V Y+ + Sbjct: 425 QIAYAVVFQWS-SFTGGDNGLIGIWPAPWAANPVA-----------------FYYLTLAL 466 Query: 196 IIGGIFSF--LQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGVMYT 253 GGI + + F FG +RA +GIN+ F +A AG+AG +Y Sbjct: 467 CGGGILAVRRITFAPFGYTLRACRDSALRADSIGINLSSHRWAGFALAGFFAGIAGSLYA 526 Query: 254 PINSPNY--HMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIPGI 311 + + + + V V+V++GG+ +L G V+ + + +++ S Sbjct: 527 FLKGSVFPDTISIATSVDGLVMVLLGGVQTLTGPVVGALV------YKTLHVTISSYTDQ 580 Query: 312 DQIIIYVVAIIILLTRPRGLMG 333 + + V+ I++++ P+G+ G Sbjct: 581 WRTALGVIIIVLVVAFPQGISG 602 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: 530 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 4 Length of query: 340 Length of database: 618 Length adjustment: 33 Effective length of query: 307 Effective length of database: 585 Effective search space: 179595 Effective search space used: 179595 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: 51 (24.3 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