Align L-lactate permease (characterized, see rationale)
to candidate 208540 DVU3026 L-lactate permease family protein
Query= uniprot:L0GFN1 (564 letters) >MicrobesOnline__882:208540 Length = 570 Score = 478 bits (1229), Expect = e-139 Identities = 256/569 (44%), Positives = 355/569 (62%), Gaps = 20/569 (3%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS LLAL A PIL+A ++++G+RWPA++AMPL +L + VW++ + A TLQ Sbjct: 1 MSLELLALVALLPILVALVLMVGMRWPATKAMPLSWLVCVLGAIGVWNLPAGYVTALTLQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 G+V +G+L I+FGAI++L TL++SGG+ I+ G +S D+RIQAIII ++F FIEGA Sbjct: 61 GIVTAIGVLIIVFGAIIILYTLQYSGGMETIQYGMQNVSRDKRIQAIIIGYMFAAFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVG-------INSGL 173 +GFGTPAA+AAPLL+++GFP +AA ++ ++ S VSFGAVGTPI++G + + Sbjct: 121 AGFGTPAALAAPLLLSLGFPPLAAAVICLVFNSFCVSFGAVGTPILIGLKFLAPLVKDAV 180 Query: 174 DTATIGAQLVAQGSSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGF 233 T G GS + + I I H + ++P+ M+ LTRF+G+ KSW GF Sbjct: 181 TAGTPGLNFTDFGS----FAKVIGQWATIMHGFMIVILPIFMLGFLTRFYGQNKSWSEGF 236 Query: 234 EVLPFAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFAD 293 + F +FA ++F +PY F+GPEFPSL+GGLVGL I+ A+ F P+ TWDF Sbjct: 237 KAWKFCVFAAVSFAVPYFIFAWFVGPEFPSLIGGLVGLGIIVAGAKRGFCVPEETWDFGP 296 Query: 294 AKEWPAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSI 351 W EW GTI+ MS F+AWLPY+L+GAILV++RV P + L + I Sbjct: 297 QSTWDPEWTGTIKTAAKTEFKAHMSQFKAWLPYILIGAILVVTRV-PSLGLKGFLSAQKI 355 Query: 352 AFANILGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGF 410 F NILG G++A I+ LYLPG I +V L+T LHGM +K A ES + + Sbjct: 356 PFDNILGFKGVSASIDYLYLPGTIPFTLVALLTILLHGMSGDAVKRAWSESFAKMKAPTI 415 Query: 411 VLLFTVPMVRILINSGV-----NGAELASMPIVMARYVADSVGSIYPLLAPAVGALGAFL 465 L F V +V I SGV N SMP+ MA+ VA G+ +P+LA VG LGAF+ Sbjct: 416 ALFFAVALVSIFRGSGVADVALNPNNYPSMPLAMAKAVAALAGNAWPMLASYVGGLGAFI 475 Query: 466 AGSNTVSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGR 525 GSNTVS+++F++FQ+GVA L + ++VA Q VG A GNMV IHN+VA A VGL GR Sbjct: 476 TGSNTVSDLLFAEFQWGVAAQLELPRQIIVAAQVVGGAMGNMVCIHNIVAVCAVVGLAGR 535 Query: 526 EGSTLRKTIWPTLYYVLFTGVIGLIAIYV 554 EG L++T WP + Y L G+I + +V Sbjct: 536 EGMILKRTFWPFMLYGLVVGIIASLMCFV 564 Lambda K H 0.326 0.140 0.415 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: 1027 Number of extensions: 60 Number of successful extensions: 6 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: 564 Length of database: 570 Length adjustment: 36 Effective length of query: 528 Effective length of database: 534 Effective search space: 281952 Effective search space used: 281952 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