Align D-lactate transporter, permease component 1 (characterized)
to candidate RR42_RS20265 RR42_RS20265 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS20265 Length = 342 Score = 178 bits (451), Expect = 2e-49 Identities = 117/339 (34%), Positives = 167/339 (49%), Gaps = 44/339 (12%) Query: 35 LAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSMN 94 LA YP + + + F +FA FN+L G TG LSFGHAAF G +Y+A K + Sbjct: 35 LAPMAGAYPVFVLKVLCFALFACAFNLLIGYTGLLSFGHAAFFGGAAYTAGHAMKAWGVT 94 Query: 95 VVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGETGL 154 +VL + L V+GY+++RR GIYFS++TLA AQM F V P T GE GL Sbjct: 95 PEVGLVLGTLAGALIGYVVGYIAIRRQGIYFSMITLALAQMLFFFCLQV--PYTGGEDGL 152 Query: 155 QLTLDDPRVLGVSATADGSIPVTSLFG-LEMRSTFEMVVGPWAFQFNAGYYLCALILLAA 213 Q IP LFG L + + + YY+ I++AA Sbjct: 153 Q-----------------GIPRGKLFGVLSLANDLTL------------YYVALAIIVAA 183 Query: 214 FYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDP 273 F L +R SPFG +LKA+K N+ R G +T + L FV+S +GLAG + A + Sbjct: 184 FALIVRTVHSPFGQILKAIKENEPRTISLGYDTDRFKLMVFVLSAALSGLAGSIKALVLG 243 Query: 274 LAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHSWFSFMP 333 A + W+ SG V+LMT++GG GTL GP++GA + EN I F Sbjct: 244 FATLTDVHWSMSGSVILMTLVGGLGTLSGPLVGAFVVVALENKLGDIGT------FLAST 297 Query: 334 DGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLV 372 GIE +G+ + G++F++ V+ G++ Sbjct: 298 TGIE------WFNSLGESVTMVTGVIFVICVLTFRRGIM 330 Lambda K H 0.327 0.143 0.435 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: 455 Number of extensions: 36 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: 400 Length of database: 342 Length adjustment: 30 Effective length of query: 370 Effective length of database: 312 Effective search space: 115440 Effective search space used: 115440 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: 49 (23.5 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