Align L-lactate permease (characterized, see rationale)
to candidate 208540 DVU3026 L-lactate permease family protein
Query= uniprot:A0KZB2 (547 letters) >MicrobesOnline__882:208540 Length = 570 Score = 390 bits (1002), Expect = e-113 Identities = 219/564 (38%), Positives = 334/564 (59%), Gaps = 32/564 (5%) Query: 4 LQLLASLTPVISVMIFLVLLRMPASKAMPISMIITALAAVFIWQMDTTLLAASVLEGLLS 63 L L +L P++ ++ +V +R PA+KAMP+S ++ L A+ +W + + A L+G+++ Sbjct: 5 LLALVALLPILVALVLMVGMRWPATKAMPLSWLVCVLGAIGVWNLPAGYVTALTLQGIVT 64 Query: 64 AITPLTIIFGAVFLLNTLKYSGAMDTIRAGFTNISADARVQVIIICWLFGAFIEGSAGFG 123 AI L I+FGA+ +L TL+YSG M+TI+ G N+S D R+Q III ++F AFIEG+AGFG Sbjct: 65 AIGVLIIVFGAIIILYTLQYSGGMETIQYGMQNVSRDKRIQAIIIGYMFAAFIEGAAGFG 124 Query: 124 TPAAIGAPLLVLLGVPPVAAAVVALIADSACVSFGAIGLPVLFGM-------EQGLTQGG 176 TPAA+ APLL+ LG PP+AAAV+ L+ +S CVSFGA+G P+L G+ + +T G Sbjct: 125 TPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGLKFLAPLVKDAVTAGT 184 Query: 177 VSLAAEQFAAHGGSYVGYARFIVMHMITIDLITGTLIPLVMVTILTGFFGRNKSFKEGLA 236 L F + +A +MH I ++P+ M+ LT F+G+NKS+ EG Sbjct: 185 PGLNFTDFGSFAKVIGQWA--TIMHGFMI-----VILPIFMLGFLTRFYGQNKSWSEGFK 237 Query: 237 IWKFAIFAGLAFTVPAWIINYLAGPEFPSVIGSLVGMALVIPVARKGYLLPKTPWNDFAE 296 WKF +FA ++F VP +I + GPEFPS+IG LVG+ +++ A++G+ +P+ W DF Sbjct: 238 AWKFCVFAAVSFAVPYFIFAWFVGPEFPSLIGGLVGLGIIVAGAKRGFCVPEETW-DFGP 296 Query: 297 NDS---------QEGAKIETTAKFSQIAAWTPYIIMAALLVLSRTVA-PLKAWLSSFNIS 346 + + AK E A SQ AW PYI++ A+LV++R + LK +LS+ I Sbjct: 297 QSTWDPEWTGTIKTAAKTEFKAHMSQFKAWLPYILIGAILVVTRVPSLGLKGFLSAQKIP 356 Query: 347 WTGLMGTE-LKASFATLYAPGAF-FVAVCILGFFLFKMKSPAIKQSIGVSCKSMLPTIIS 404 + ++G + + AS LY PG F V +L L M A+K++ S M I+ Sbjct: 357 FDNILGFKGVSASIDYLYLPGTIPFTLVALLTILLHGMSGDAVKRAWSESFAKMKAPTIA 416 Query: 405 LGASVPMVKIFLNSGV-----NGAGLASMPVALADMLGQSMGAVWAWMAPIVGIFGAFLS 459 L +V +V IF SGV N SMP+A+A + G W +A VG GAF++ Sbjct: 417 LFFAVALVSIFRGSGVADVALNPNNYPSMPLAMAKAVAALAGNAWPMLASYVGGLGAFIT 476 Query: 460 GSATFSNMMFSSLQYSVADNIGMNHTLVLALQGIGANAGNMMCVMNVVAAATVVGMAGRE 519 GS T S+++F+ Q+ VA + + +++A Q +G GNM+C+ N+VA VVG+AGRE Sbjct: 477 GSNTVSDLLFAEFQWGVAAQLELPRQIIVAAQVVGGAMGNMVCIHNIVAVCAVVGLAGRE 536 Query: 520 SEIIRKTMPVAIGYALLAGTIATL 543 I+++T + Y L+ G IA+L Sbjct: 537 GMILKRTFWPFMLYGLVVGIIASL 560 Lambda K H 0.326 0.138 0.413 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: 945 Number of extensions: 57 Number of successful extensions: 5 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: 547 Length of database: 570 Length adjustment: 36 Effective length of query: 511 Effective length of database: 534 Effective search space: 272874 Effective search space used: 272874 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 (21.7 bits) S2: 53 (25.0 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