Align L-lactate and D-lactate permease (lctP family) (characterized)
to candidate Pf1N1B4_4246 L-lactate permease
Query= reanno::pseudo5_N2C3_1:AO356_07550 (564 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4246 Length = 585 Score = 479 bits (1232), Expect = e-139 Identities = 255/576 (44%), Positives = 357/576 (61%), Gaps = 28/576 (4%) Query: 4 WQQLYSPLGSLGLSALAAVIPIVFFFLALAVFRLKGHVAGSITLALAIAVAIFAFNMPAD 63 WQQ+Y P + LS + A +P+V +LA F +K H+A + L A+ +AIFAF MPA+ Sbjct: 3 WQQIYDPFDNPMLSTIMAAVPVVVMLASLAFFHIKAHLAALLALGSALLIAIFAFGMPAN 62 Query: 64 MAFAAAGYGFAYGLWPIAWIIVAAVFLYKLTVKSGQFEVIRSSVLSITDDQRLQVLLIGF 123 MA +AA YG A GL PI WI++ +FL++LT ++G F+V++ S+ ITDD+RLQ+LLI F Sbjct: 63 MAGSAALYGAANGLLPIGWIVLNIIFLHRLTTENGSFKVLQDSLARITDDRRLQLLLIAF 122 Query: 124 CFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGALGIPIIVAGQV 183 CFGAF EGAAGFG PVA+T A+L+GLGF+PL A+GL LIANTAPVAFGALG PII +V Sbjct: 123 CFGAFFEGAAGFGTPVAVTGAILIGLGFSPLAASGLALIANTAPVAFGALGTPIITLAKV 182 Query: 184 TGIDAFKIGAMTGRQLPLLSLFVPFWLVFMMDGLRGVRETWPAALVAGLSFAITQYFTSN 243 TG+D ++ M GRQLP S+ VPFWL++ G R + E WPA L+AG+SFA+ Q+ SN Sbjct: 183 TGLDEMELSMMVGRQLPFFSVIVPFWLIWAFAGWRKMLEIWPAILIAGVSFAVPQFLVSN 242 Query: 244 FIGPELPDITSALASLISLTLFLKVWQPKRT-AGAQIAGATSSATVTASVGGFGQPRSTV 302 + GP L D+ +AL S+ LT FLKVW+P A ++G ++ V V +P +T Sbjct: 243 YHGPMLVDVIAALISMACLTGFLKVWKPATVHTSAALSGRADNSRV--DVDPDEEPSATF 300 Query: 303 ASPYSLGEIIKAWSPFLILTVLVTIWTLKPFKAMF----------------------AAG 340 AS + +++AW P++ILTV V W + FK +F Sbjct: 301 ASD-AKPAVMRAWMPWIILTVFVFAWGTQSFKNLFDTRPVMDPQTHSAKLDPQGKPMREA 359 Query: 341 GSMYGWVFNFAIPHLDQMVIKVAPIVINPTAIPAVFKLDPISATGTAIFFSALISMLVLK 400 ++ F H Q + KV P+V A++K + ++TG+ I +AL+ L++ Sbjct: 360 NPIFAPTLTFTTIH--QQIEKVPPVVPVAKTEDAIYKFNWFTSTGSGILLAALLGGLLMG 417 Query: 401 INIKTGLTTFKETLFELRWPILSIGMVLAFAFVTNYSGMSSTMALVLAGTGAAFPFFSPF 460 +I L + TL+ +R+ +++I +LA F+T YSG+ +TM L A TG +P F Sbjct: 418 YSIPQLLHHYLRTLWVVRYSLITIVAMLALGFLTRYSGLDATMGLAFAATGIFYPMFGTL 477 Query: 461 LGWLGVFLTGSDTSSNALFSSLQATTAHQIGVNDTLLVAANTSGGVTGKMISPQSIAVAC 520 LGWLGV LTGSDT+SN LF LQ TA Q+G++ L+ AAN+SGGV GKM+ QSI VA Sbjct: 478 LGWLGVALTGSDTASNVLFGGLQRVTAEQLGLSPVLMAAANSSGGVMGKMVDAQSIVVAS 537 Query: 521 AATGLVGKESDLFRFTLKHSLFFATIVGLITLAQAY 556 AT G E ++ R+ HS+ A +VG + QAY Sbjct: 538 TATRWYGHEGEILRYVFFHSVVLAILVGGLVTLQAY 573 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: 867 Number of extensions: 35 Number of successful extensions: 2 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: 585 Length adjustment: 36 Effective length of query: 528 Effective length of database: 549 Effective search space: 289872 Effective search space used: 289872 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