Align D-lactate transporter, permease component 1 (characterized)
to candidate HSERO_RS23975 HSERO_RS23975 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS23975 Length = 326 Score = 171 bits (432), Expect = 4e-47 Identities = 115/337 (34%), Positives = 163/337 (48%), Gaps = 51/337 (15%) Query: 12 LLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSF 71 + V+ IL L APF + YP + + + F +FA FN+L G TG LSF Sbjct: 7 IAVLLILLLAAPFGI---------------YPVFLMKMLCFALFACAFNLLIGYTGLLSF 51 Query: 72 GHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLA 131 GHAAFLG Y K+ + +++ + L LV+G +++RR GIYF+++TLA Sbjct: 52 GHAAFLGWAGYMCGQALKVWGLPTELGLIIGTLTGALIGLVMGLLAIRRQGIYFTMITLA 111 Query: 132 FAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFG-LEMRSTFEM 190 AQM F +A + P T GE GLQ +P L G L + S + Sbjct: 112 LAQMLFFVA--LQAPFTGGEDGLQ-----------------GVPRGKLLGFLNLESDMTL 152 Query: 191 VVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYT 250 YY+ I +A F L +R SPFG +LKA+K N+ R G + Y Sbjct: 153 ------------YYVVLAIAVAGFALIVRTIHSPFGQVLKAIKENEPRAISLGYDVARYK 200 Query: 251 LAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFI 310 L AFV+S +GLAG + + W+ SG VVLMT++GG GT++GP++GA I Sbjct: 201 LLAFVLSAGLSGLAGATKTLVLGFETLTDVHWSMSGLVVLMTLVGGLGTILGPIVGAVII 260 Query: 311 KYFENIFSKIN---DNVLH-SWFSFMPDGIEDAMVFI 343 EN I +V H WF+ + D + FI Sbjct: 261 IMLENKLGDIGAWLASVTHIDWFNTLGDSVTIVTGFI 297 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: 443 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: 326 Length adjustment: 29 Effective length of query: 371 Effective length of database: 297 Effective search space: 110187 Effective search space used: 110187 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