Align D-lactate transporter, permease component 1 (characterized)
to candidate GFF1060 Psest_1093 ABC-type branched-chain amino acid transport system, permease component
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__psRCH2:GFF1060 Length = 335 Score = 169 bits (427), Expect = 1e-46 Identities = 117/384 (30%), Positives = 175/384 (45%), Gaps = 89/384 (23%) Query: 6 KKDKTLLLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGL 65 ++ K V+ ++ L AP A YP + + + F +FA FN+L G Sbjct: 27 RRQKVFYAVLLVIALLAPL---------------AVYPVFLMKLLCFALFACAFNLLLGY 71 Query: 66 TGYLSFGHAAFLGVGSYSAVWMFKLLS-----MNVVPAIVLSVIVAGLFALVIGYVSLRR 120 G LSFGHAAF G Y +M S + ++ + S ++ GLF G +++RR Sbjct: 72 AGLLSFGHAAFFATGGYITGYMLSSYSGLSTELGILAGTLASTVLGGLF----GMLAIRR 127 Query: 121 SGIYFSILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLF 180 GIYF+++TLA AQ+ F + V P T GE GLQ +P LF Sbjct: 128 QGIYFAMITLALAQLVFFVF--VQAPFTGGENGLQ-----------------GVPRGHLF 168 Query: 181 GL-EMRSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRM 239 GL +M++ M YY + + F + R SP+G +LKA++ N+ R Sbjct: 169 GLVDMKNNMAM------------YYFVLAVFVLGFAIIQRTIHSPYGQVLKAIRENEPRA 216 Query: 240 NYTGLNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGT 299 G N + L AFVIS AGLAG + LA W SGEV+LMT+LGG GT Sbjct: 217 VSLGYNVDRHKLLAFVISAALAGLAGATKTVVFQLASLTDAHWHMSGEVILMTLLGGVGT 276 Query: 300 LIGPVLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFIVHPFIGKGWHLTLGIL 359 ++GP++GA + + S +++ L W H+ LG++ Sbjct: 277 ILGPLVGATVVVTLQ---SSLSNGPLGEWV-----------------------HVILGVI 310 Query: 360 FMLVVIFLPGGLVEGGQKLRGWIQ 383 F+L V+ G+V GW++ Sbjct: 311 FVLCVLLFRSGIV-------GWLE 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: 441 Number of extensions: 26 Number of successful extensions: 5 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: 335 Length adjustment: 30 Effective length of query: 370 Effective length of database: 305 Effective search space: 112850 Effective search space used: 112850 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