Align D-lactate transporter, permease component 1 (characterized)
to candidate AZOBR_RS08500 AZOBR_RS08500 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__azobra:AZOBR_RS08500 Length = 327 Score = 168 bits (425), Expect = 2e-46 Identities = 110/310 (35%), Positives = 151/310 (48%), Gaps = 45/310 (14%) Query: 12 LLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSF 71 L V+ ++ + AP++L YP + + + F +FA FN+L G G LSF Sbjct: 28 LAVLLLVLIAAPYVL---------------YPVFVMKVLCFALFACAFNLLIGFAGLLSF 72 Query: 72 GHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLA 131 GHAAF G +Y K+ + I+L A L G +++RR GIYF+++TLA Sbjct: 73 GHAAFFGGAAYITAHTVKVWGLPPELGILLGTAFAATLGLAFGALAIRRQGIYFAMITLA 132 Query: 132 FAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEMRSTFEMV 191 +QM F +A + T GE G+Q ++P LFG+ S Sbjct: 133 LSQMVFFMALQL--KFTGGEDGIQ-----------------AVPRGHLFGVIDLS----- 168 Query: 192 VGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTL 251 Q A YY + L F + R SPFG +LKA++ N+ R G T Y L Sbjct: 169 ------QSMAMYYTVLAVFLFGFAVIWRTVHSPFGQVLKAIRENEPRAISLGYRTDHYKL 222 Query: 252 AAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIK 311 AFV+S AGLAGG A + LA +QW SG VVLMT+LGG GTL GPV+GA + Sbjct: 223 MAFVLSATLAGLAGGTKAIVFQLATLTDVQWQMSGAVVLMTLLGGIGTLFGPVVGAALVV 282 Query: 312 YFENIFSKIN 321 EN + N Sbjct: 283 TLENYLAASN 292 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: 403 Number of extensions: 27 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: 327 Length adjustment: 29 Effective length of query: 371 Effective length of database: 298 Effective search space: 110558 Effective search space used: 110558 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