Align D-lactate transporter, permease component 2 (characterized)
to candidate BPHYT_RS21490 BPHYT_RS21490 ABC transporter permease
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__BFirm:BPHYT_RS21490 Length = 646 Score = 146 bits (369), Expect = 1e-39 Identities = 104/346 (30%), Positives = 167/346 (48%), Gaps = 65/346 (18%) Query: 4 ILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFET 63 +L+Q++NGL S L+A GL+LIFG +VNFAHG+ +M G + A ++ Sbjct: 5 LLVQLVNGLADASTLFLVAAGLSLIFGVTRIVNFAHGSFYMFGIYVAYSIA--------- 55 Query: 64 VDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLI 123 S FG GG W L++L A ++ +G ++E ++ Sbjct: 56 ---------------------SRFGHTTGGF---W---LSVLAAALVVAVLGALVEMVVL 88 Query: 124 KHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYP 183 + Y+ P +L TF L ++ ++ + +G + P L G V+ +G + P Sbjct: 89 RRIYQAPELFHLLATFALVLIFRDAALWLWGPEDLFGPRAPHLAGAVDF---LGHPL--P 143 Query: 184 VWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAA 243 + + V++ ++ L T +G +VRA DRE +G LGIN FT +F + A Sbjct: 144 TYDIALIVIGPVVLLLLWYALTRTRWGTLVRAATQDREMLGALGINQAWLFTGVFFVGAF 203 Query: 244 VAGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNE 303 +AGL G + P S N + ++ + +FVVVVVGGMGS+PGA +A ++ E Sbjct: 204 LAGLGGALQGPRMSANLSLDLETIGNAFVVVVVGGMGSIPGAFIAALIIA---------E 254 Query: 304 IKSLIPGIDQIII---------------YVVAIIILLTRPRGLMGR 334 IK+L GI + I +VV ++L+ RP GL+GR Sbjct: 255 IKALCIGIGHVTIFGVGLSLSRFTLVAEFVVMAVVLVVRPWGLLGR 300 Score = 39.3 bits (90), Expect = 3e-07 Identities = 75/336 (22%), Positives = 131/336 (38%), Gaps = 69/336 (20%) Query: 1 MDAILLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLS 60 M +L++IL + L A L I G G+ +F H A F +GA+ A +VL+L Sbjct: 346 MPVLLVEILIAV-------LFATSLHFIMGPGGMHSFGHAAYFGLGAYGAALFLKVLNLP 398 Query: 61 FETVDETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMER 120 E LG L V V WF + G + L + FA I+ V + + Sbjct: 399 MEAA-----LLLGPLLAVAGALVFGWFCVRLSGV---YLAMLTLAFA-QIVWSVVFQWDD 449 Query: 121 GLIKHFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDI 180 VT G +L + +N + +P A V + ++IG Sbjct: 450 ----------------VTGGSNGILG-----LWPSNWLSSPV--AFYYVTLVCAVIG--- 483 Query: 181 VYPVWRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGI 240 VW + + F+ G +RA +GI++ R F I Sbjct: 484 ---VW--------------LLRKMLFSPLGYAMRASRDSVLRAEAIGIDVKRVQWAAFVI 526 Query: 241 AAAVAGLAGVMYT---PINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLES 297 A+ GLAG +Y SP + + V V+V++GG+ +L G ++ + Sbjct: 527 ASLFCGLAGSLYAFSKGTISPEV-ISVSRSVDGLVMVLLGGLQTLTGPIVGAAV------ 579 Query: 298 FASMNEIKSLIPGIDQIIIYVVAIIILLTRPRGLMG 333 F + + + Q ++ +++++ P+G++G Sbjct: 580 FTWLQDTVARQTDYWQALLGFAILLLVIAFPQGIVG 615 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: 499 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 340 Length of database: 646 Length adjustment: 33 Effective length of query: 307 Effective length of database: 613 Effective search space: 188191 Effective search space used: 188191 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