Align L-lactate permease (characterized, see rationale)
to candidate RR42_RS14610 RR42_RS14610 lactate permease
Query= uniprot:Q8EIL2 (545 letters) >FitnessBrowser__Cup4G11:RR42_RS14610 Length = 558 Score = 483 bits (1243), Expect = e-141 Identities = 246/552 (44%), Positives = 350/552 (63%), Gaps = 15/552 (2%) Query: 3 WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62 WTQ Y PLGSL L+ + A +P+ AL L+ H+A L L++ + +A + MP + Sbjct: 2 WTQVYDPLGSLALSTLAAGIPVAVLLAALAFFHLQAHLAAGLALVVGVVIASAVFGMPAA 61 Query: 63 IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122 +A +A G + GL+PI WI++ +FL+++T G F+++++S+ +TED+RLQ+LLV F Sbjct: 62 MAGKAAGLGIASGLFPIGWIVLNIIFLHRLTTINGSFKVLQNSISGITEDRRLQLLLVAF 121 Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182 SFGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGA+G P+I V Sbjct: 122 SFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGAPLIGLSAV 181 Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242 + LD H+ + GRQLP S++VPFWLI G+RG+ WPA LVAGV+FAV QFL SN Sbjct: 182 TGLDLLHLSAMVGRQLPFFSLLVPFWLIWAFAGLRGMLAIWPAILVAGVTFAVPQFLVSN 241 Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQR-------------AVTPKST 289 + GP L D+ +ALVS+ CLTLFLKVW+PKEI+T + + R A S Sbjct: 242 YHGPWLVDVIAALVSMGCLTLFLKVWKPKEIWTSTRILGRRDDSKVDDPEAVAAEARASA 301 Query: 290 FSNG-QIFKAWSPFIILTAIVTLWSIKDV-QLALSFATISIEVPYLHNLVIKTAPIVAKE 347 S G + KAW P++ILT V +W + + +L +P L V K P+V K Sbjct: 302 ASAGISVVKAWMPWVILTVFVFVWGVPEFKKLMDGLWQWKFPIPGLDKAVFKVPPVVPKA 361 Query: 348 TPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNALTSFKDTLIELRFPILSIGLVLA 407 T A++ N+L GT IL++ ++ +++ S+ + + +T+ +++ +L+I + Sbjct: 362 TAEGAVFTFNVLSMAGTGILVSGILGGLLMGYSLPRLVREYWETIKLVKYSLLTICAMFG 421 Query: 408 FAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVFLTGSDTSSNALFGALQANTANQ 467 ++ YSGL +TL L A TGV +P F LGWLGV LTGSDT+SN LFG LQ TA Q Sbjct: 422 VGYLTRYSGLDATLGLAFAHTGVLYPLFGTMLGWLGVALTGSDTASNVLFGGLQKTTAEQ 481 Query: 468 IGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAGKESDLFRFTLKHSLFFCTFIGV 527 +G++P L+ +AN++GGV GKMI QSI VA AT G E ++ R+ HS+ +G+ Sbjct: 482 LGLSPILMASANSSGGVMGKMIDAQSIVVASTATKWYGHEGEILRYVFFHSIALAILVGL 541 Query: 528 LTVLQAYIVPWT 539 LQAY+ P+T Sbjct: 542 FITLQAYVHPFT 553 Lambda K H 0.327 0.140 0.419 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: 948 Number of extensions: 46 Number of successful extensions: 4 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: 545 Length of database: 558 Length adjustment: 36 Effective length of query: 509 Effective length of database: 522 Effective search space: 265698 Effective search space used: 265698 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