Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate RR42_RS14610 RR42_RS14610 lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__Cup4G11:RR42_RS14610 Length = 558 Score = 502 bits (1292), Expect = e-146 Identities = 265/565 (46%), Positives = 361/565 (63%), Gaps = 12/565 (2%) Query: 4 WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63 W Q+Y PLGSL LS LAA IP+ ALA F L+ H+A + L + + +A F MPA Sbjct: 2 WTQVYDPLGSLALSTLAAGIPVAVLLAALAFFHLQAHLAAGLALVVGVVIASAVFGMPAA 61 Query: 64 MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123 MA AAG G A GL+PI WI++ +FL++LT +G F+V+++S+ IT+D+RLQ+LL+ F Sbjct: 62 MAGKAAGLGIASGLFPIGWIVLNIIFLHRLTTINGSFKVLQNSISGITEDRRLQLLLVAF 121 Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183 FGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGALG P+I V Sbjct: 122 SFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGAPLIGLSAV 181 Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243 TG+D + AM GRQLP SL VPFWL++ GLRG+ WPA LVAG++FA+ Q+ SN Sbjct: 182 TGLDLLHLSAMVGRQLPFFSLLVPFWLIWAFAGLRGMLAIWPAILVAGVTFAVPQFLVSN 241 Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRT-AGAQIAGATSSATVTASVGGFGQPRSTV 302 + GP L D+ +AL S+ LTLFLKVW+PK +I G + V + R++ Sbjct: 242 YHGPWLVDVIAALVSMGCLTLFLKVWKPKEIWTSTRILGRRDDSKVDDPEAVAAEARASA 301 Query: 303 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMFAAGGSMYG-WVFNFAIPHLDQMVIK 361 AS ++KAW P++ILTV V +W + FK + M G W + F IP LD+ V K Sbjct: 302 ASAGI--SVVKAWMPWVILTVFVFVWGVPEFKKL------MDGLWQWKFPIPGLDKAVFK 353 Query: 362 VAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLKINIKTGLTTFKETLFELRWPI 421 V P+V TA AVF + +S GT I S ++ L++ ++ + + ET+ +++ + Sbjct: 354 VPPVVPKATAEGAVFTFNVLSMAGTGILVSGILGGLLMGYSLPRLVREYWETIKLVKYSL 413 Query: 422 LSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPFLGWLGVFLTGSDTSSNALFSS 481 L+I + ++T YSG+ +T+ L A TG +P F LGWLGV LTGSDT+SN LF Sbjct: 414 LTICAMFGVGYLTRYSGLDATLGLAFAHTGVLYPLFGTMLGWLGVALTGSDTASNVLFGG 473 Query: 482 LQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVACAATGLVGKESDLFRFTLKHSL 541 LQ TTA Q+G++ L+ +AN+SGGV GKMI QSI VA AT G E ++ R+ HS+ Sbjct: 474 LQKTTAEQLGLSPILMASANSSGGVMGKMIDAQSIVVASTATKWYGHEGEILRYVFFHSI 533 Query: 542 FFATIVGLITLAQAYW--FTGMLVH 564 A +VGL QAY FT M++H Sbjct: 534 ALAILVGLFITLQAYVHPFTQMVIH 558 Lambda K H 0.327 0.139 0.422 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: 882 Number of extensions: 52 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: 564 Length of database: 558 Length adjustment: 36 Effective length of query: 528 Effective length of database: 522 Effective search space: 275616 Effective search space used: 275616 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