Align D-lactate transporter, permease component 1 (characterized)
to candidate Ac3H11_1431 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1431 Length = 333 Score = 179 bits (455), Expect = 8e-50 Identities = 118/362 (32%), Positives = 178/362 (49%), Gaps = 57/362 (15%) Query: 32 GSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSYSAVWMFKLL 91 G +A F YP + + + F +FA FN+L G TG LSFGHAAFLG +Y A K+ Sbjct: 17 GLVVAPFLGAYPVFVMKLMCFALFASAFNLLLGFTGLLSFGHAAFLGGAAYVAGHAIKVW 76 Query: 92 SMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYSVLTPITNGE 151 + ++L L L+ G++++RR GIYFS++TLA AQM F T GE Sbjct: 77 GLTPEVGLLLGTAGGALLGLLFGWLAIRRQGIYFSMITLALAQMLFFACLQA--KFTGGE 134 Query: 152 TGLQLTLDDPRVLGVSATADGSIPVTSLFG-LEMRSTFEMVVGPWAFQFNAGYYLCALIL 210 GLQ +P LFG ++++S M YY+ +I+ Sbjct: 135 DGLQ-----------------GVPRGKLFGVIDLQSDLVM------------YYVALVIV 165 Query: 211 LAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYAGLAGGLMAS 270 AF L +R SPFG +LK +K N+ R G +T + L AFV+S AGLAG L Sbjct: 166 ALAFLLIVRTIHSPFGQVLKGIKENEPRAISLGYDTHRFKLLAFVLSAALAGLAGSLKTL 225 Query: 271 MDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKINDNVLHS--- 327 + A + WTASG+V+LMT++GG GTL GP++G+ + EN + N+L + Sbjct: 226 VLGFATLSDVHWTASGQVILMTLVGGLGTLSGPLIGSAVVVLLENKIGEFG-NLLAALTS 284 Query: 328 --WFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIFLPGGLVEGGQKLRGWIQGR 385 WF +G+ + G++F++ V+ G++ ++ W+ R Sbjct: 285 VEWFK----------------TLGESVTMVTGLIFVICVLAFRRGIM---GEIIAWLAQR 325 Query: 386 KA 387 +A Sbjct: 326 RA 327 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: 463 Number of extensions: 31 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: 333 Length adjustment: 30 Effective length of query: 370 Effective length of database: 303 Effective search space: 112110 Effective search space used: 112110 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