Align L-lactate permease (characterized, see rationale)
to candidate 207944 DVU2451 L-lactate permease family protein
Query= uniprot:L0GFN1 (564 letters) >MicrobesOnline__882:207944 Length = 570 Score = 474 bits (1220), Expect = e-138 Identities = 253/568 (44%), Positives = 364/568 (64%), Gaps = 18/568 (3%) Query: 1 MSNGLLALFAFTPILLAAIMLIGLRWPASRAMPLVFLFTAAIGLFVWDMSVNRIIASTLQ 60 MS LLAL A PIL+A ++++GLR+PA+RAMPL +L + VW++ + A TLQ Sbjct: 1 MSIELLALVALLPILVALVLMVGLRFPATRAMPLAWLVCVIGAIGVWNLPAGYVSALTLQ 60 Query: 61 GLVITLGLLWIIFGAILLLNTLKHSGGITAIRAGFTTISPDRRIQAIIIAWLFGCFIEGA 120 G+V +G+L I+FGAI++L TL++SGG+ I+ G +S D+RIQAII+ ++F FIEGA Sbjct: 61 GIVTAIGVLIIVFGAIIILYTLQYSGGMETIQYGMQNVSRDKRIQAIIVGYMFAAFIEGA 120 Query: 121 SGFGTPAAIAAPLLVAVGFPAMAAVLLGMLVQSTPVSFGAVGTPIVVGINSGLDTATIGA 180 +GFGTPAA+AAPLL+++GFP +AA ++ ++ S PVSFGAVGTP+++G+ A + Sbjct: 121 AGFGTPAALAAPLLLSLGFPPLAAAVICLVFNSFPVSFGAVGTPVLIGLKF---LAPLTQ 177 Query: 181 QLVAQG------SSWNAYLQQITSSVAITHAIVGTVMPLVMVLMLTRFFGKEKSWKAGFE 234 + VAQG + + ++ + I + H + ++P+ M+ LTR+FG++KSW GF+ Sbjct: 178 EAVAQGIPGLNFTDFGSFAKVIGQWATLMHGPMIVILPIFMLGFLTRYFGEKKSWVEGFK 237 Query: 235 VLPFAIFAGLAFTLPYAATGIFLGPEFPSLLGGLVGLAIVTTAARFKFLTPKTTWDFADA 294 F +F+ +AF +PY F+GPEFPSL+GGLVGL I+ A+ F P+T WDF Sbjct: 238 AWKFCVFSAVAFAVPYYVFAWFVGPEFPSLIGGLVGLGIIVAGAKRGFCVPETPWDFGPQ 297 Query: 295 KEWPAEWLGTIEMKLDEMAARPMSAFRAWLPYVLVGAILVISRVFPQ--VTAALKSVSIA 352 W AEW G+I + MS FRAWLPYVL+G ILV++R+ P+ + L + I Sbjct: 298 SSWDAEWTGSIRTAANTEFKAHMSQFRAWLPYVLIGLILVVTRI-PELGLKGFLSAQKIP 356 Query: 353 FANILGETGINAGIEPLYLPGGI-LVMVVLITFFLHGMRVSELKAAVKESSGVLLSAGFV 411 F +ILG G++A I+ LYLPG I +V L+T LHGM+ +K A ES + S Sbjct: 357 FNDILGYKGVSASIDYLYLPGTIPFTLVALLTILLHGMKGDAVKRAWGESIAKMKSPTIA 416 Query: 412 LLFTVPMVRILINSGVNGAEL-----ASMPIVMARYVADSVGSIYPLLAPAVGALGAFLA 466 L F V +V I SGV A L SMP+ MA+ VA G+ +P+LA VG LG+F+ Sbjct: 417 LFFAVALVSIFRGSGVVDAALNPNAYPSMPLAMAKAVAAVAGNAWPMLASFVGGLGSFIT 476 Query: 467 GSNTVSNMMFSQFQFGVAQSLGISGAMVVATQAVGAAAGNMVAIHNVVAASATVGLLGRE 526 GSNTVS+++F++FQ+GVA L + ++VA Q VG A GNMV IHN+VA A VGL GRE Sbjct: 477 GSNTVSDLLFAEFQWGVAAQLSMPRQVIVAAQVVGGAMGNMVCIHNIVAVCAVVGLTGRE 536 Query: 527 GSTLRKTIWPTLYYVLFTGVIGLIAIYV 554 G+ L++ P + Y + GV+ + +V Sbjct: 537 GTLLKRCFLPFVLYGVVVGVVASLMSFV 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: 1020 Number of extensions: 67 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