Align D-lactate transporter, permease component 1 (characterized)
to candidate RR42_RS26440 RR42_RS26440 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS26440 Length = 352 Score = 172 bits (436), Expect = 1e-47 Identities = 109/318 (34%), Positives = 159/318 (50%), Gaps = 38/318 (11%) Query: 34 ALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLLSM 93 ALA YP L + + F +FA FN+L G TG LSFGHAAF G +Y+ ++ K L Sbjct: 19 ALAPLLGAYPVLAMKLMCFALFACAFNLLLGFTGLLSFGHAAFFGGAAYACGYVMKSLHA 78 Query: 94 NVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGETG 153 ++ L L G +++RR GIYF+++TLA AQM + + + P+T GE G Sbjct: 79 TPELGLLAGTAFGALLGLAFGALAIRRQGIYFAMVTLALAQMFY--FFCLQAPVTGGEDG 136 Query: 154 LQLTLDDPRVLGVSATADGSIPVTSLFGL-EMRSTFEMVVGPWAFQFNAGYYLCALILLA 212 LQ ++P SLFGL + M YY+ +++ A Sbjct: 137 LQ-----------------AVPRGSLFGLISLEGDLTM------------YYVVSIVAGA 167 Query: 213 AFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMASMD 272 A L R+ SPFG +L+A+K N+ R G +T + L AFV+S AGLAG L + Sbjct: 168 ALLLIARVVNSPFGQVLRAIKENEPRAISLGYDTDRFKLLAFVLSSALAGLAGALKTLVL 227 Query: 273 PLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLH----SW 328 A + W SG V+LMT++GG GTL GP+LGA I EN ++ W Sbjct: 228 GFATLTDVHWAMSGSVILMTLVGGMGTLSGPILGALVIVAVENKLGDAGSSLAAMTGVDW 287 Query: 329 FSFMPDGIE--DAMVFIV 344 F+ + + + ++F+V Sbjct: 288 FNTLGESVSMVTGLIFVV 305 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: 409 Number of extensions: 23 Number of successful extensions: 3 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: 352 Length adjustment: 30 Effective length of query: 370 Effective length of database: 322 Effective search space: 119140 Effective search space used: 119140 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: 50 (23.9 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