Align D-lactate transporter, permease component 1 (characterized)
to candidate GFF3787 Psest_3856 ABC-type branched-chain amino acid transport system, permease component
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__psRCH2:GFF3787 Length = 328 Score = 169 bits (427), Expect = 1e-46 Identities = 106/312 (33%), Positives = 157/312 (50%), Gaps = 48/312 (15%) Query: 9 KTLLLVVAILTL-FAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTG 67 +T+L+++ ++ L APF YP + + + F +FA FN+L G TG Sbjct: 19 ETVLILIGVIALALAPFYF---------------YPIFLMKVLCFALFACAFNLLLGYTG 63 Query: 68 YLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSI 127 LSFGHAAF G +Y K + I++ V A L+IG++++RR GIY ++ Sbjct: 64 ILSFGHAAFFGGAAYFTAHAVKEWGLTPELGILVGVAGAAFLGLIIGFLAIRRQGIYSTM 123 Query: 128 LTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGL-EMRS 186 +TLA +QM F + + T+GE G+Q +IP LFGL ++ Sbjct: 124 ITLALSQMFF--FFCLQASFTHGEDGIQ-----------------NIPRGHLFGLIDLEE 164 Query: 187 TFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNT 246 M Y+ + LA L R+ SP+G++L++++ N+ R G + Sbjct: 165 PLYM------------YFFVLSVFLAGMLLIWRVIHSPYGMILRSIRENENRAISLGYSV 212 Query: 247 RPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLG 306 Y L AFV+S AGLAGGL A + A + W SGEVVLMT+LGG GTL+GPV G Sbjct: 213 SRYKLGAFVMSAALAGLAGGLKALVFQFATLTDVSWQMSGEVVLMTLLGGIGTLVGPVFG 272 Query: 307 AGFIKYFENIFS 318 A + N F+ Sbjct: 273 AALVTTLGNYFA 284 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: 414 Number of extensions: 29 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: 328 Length adjustment: 29 Effective length of query: 371 Effective length of database: 299 Effective search space: 110929 Effective search space used: 110929 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