Align D-lactate transporter, permease component 2 (characterized)
to candidate 3610344 Dshi_3725 inner-membrane translocator (RefSeq)
Query= reanno::Phaeo:GFF1250 (340 letters) >FitnessBrowser__Dino:3610344 Length = 294 Score = 156 bits (395), Expect = 5e-43 Identities = 108/332 (32%), Positives = 169/332 (50%), Gaps = 53/332 (15%) Query: 7 QILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDE 66 Q+LNGL G + L+ALGLT+IFG L V+N +HG + +GA+ A+ + Sbjct: 12 QMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAYGALALAA----------- 60 Query: 67 TQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHF 126 FG V ++ VPL +MI +G V ER LI+ Sbjct: 61 --------------------FG--VNYWVLMAMVPL-------MMIPLGIVTERYLIRRV 91 Query: 127 YKRP--HADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPV 184 Y H +L+TFGL ++ ++V+K +G N + P L G +L M I P Sbjct: 92 YDGADRHVSTLLLTFGLGLIAEDVLKIIFGPNTQRPENP--LPGATDL-----MGIFIPT 144 Query: 185 WRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAV 244 +R+ + +I + + T G +VRA DR LG+ + ++ F A+ Sbjct: 145 YRLFLIAISAAVILAVAFVVYRTRLGAIVRAASFDRNMAASLGVRVGWVYSGAFAFGVAL 204 Query: 245 AGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEI 304 AGLAGV+ PI S MG DF++++F VV+VGGMGS+ GAV+AG +L +++ +S+ Sbjct: 205 AGLAGVLLAPIYSVFPTMGRDFILIAFTVVIVGGMGSIWGAVVAGIVLTQIQAISSL--- 261 Query: 305 KSLIPGIDQIIIYVVAIIILLTRPRGLMGRKG 336 + P + I++ V +++L+ RP+GL GR G Sbjct: 262 -VISPVWSEPIVFGVMVLVLMFRPQGLFGRIG 292 Lambda K H 0.329 0.147 0.439 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: 305 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 340 Length of database: 294 Length adjustment: 27 Effective length of query: 313 Effective length of database: 267 Effective search space: 83571 Effective search space used: 83571 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 (21.8 bits) S2: 48 (23.1 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