Align D-lactate transporter, permease component 1 (characterized)
to candidate AZOBR_RS16650 AZOBR_RS16650 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__azobra:AZOBR_RS16650 Length = 328 Score = 171 bits (432), Expect = 4e-47 Identities = 107/310 (34%), Positives = 157/310 (50%), Gaps = 47/310 (15%) Query: 7 KDKTLLLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLT 66 ++ +L + ++ L APF+L YP + + + F +FA FN+L G Sbjct: 26 RNAIILGIGLLIALAAPFVL---------------YPVFVMKVLCFALFACAFNLLIGFA 70 Query: 67 GYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFS 126 G LSFGHAAF G +Y K+ + +I+L + + L L G +++RR GIYF+ Sbjct: 71 GLLSFGHAAFFGGAAYITAHSAKVWGLGPEVSILLGMGFSALLGLAFGALAIRRQGIYFA 130 Query: 127 ILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFG-LEMR 185 ++TLA +QM F +A + T GE G+Q ++P LFG +++ Sbjct: 131 MITLALSQMVFFMALQL--KFTGGEDGIQ-----------------AVPRGHLFGVIDLN 171 Query: 186 STFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLN 245 ++ M YY + L F + R SPFG +LKA++ N+ R G Sbjct: 172 NSLSM------------YYFVLAVFLVGFAVVWRAVHSPFGQVLKAIRENEPRAVSLGYR 219 Query: 246 TRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVL 305 T Y L AFV+S AGLAGG A + LA + W SGEVVLMT+LGG GTL+GPV+ Sbjct: 220 TERYKLLAFVLSASLAGLAGGTKALVFQLASLTDVTWQMSGEVVLMTLLGGMGTLLGPVV 279 Query: 306 GAGFIKYFEN 315 GA + E+ Sbjct: 280 GAAIVVTLES 289 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: 428 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