Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate GFF2718 Psest_2772 MIP family channel proteins
Query= SwissProt::F9UST3 (238 letters) >FitnessBrowser__psRCH2:GFF2718 Length = 293 Score = 102 bits (254), Expect = 8e-27 Identities = 79/244 (32%), Positives = 124/244 (50%), Gaps = 24/244 (9%) Query: 4 QLIAEFMGTALMIIFGVGVHCSSVLK-GTKYRGSGHIFAITTWGFGISVALFIFGNVC-- 60 Q IAEF+GTAL+I FG G C + LK G G I I WG G+S+A+++ V Sbjct: 12 QCIAEFLGTALLIFFGTG--CVAALKLGGAELGLWEISII--WGIGVSMAVYLAAGVSGA 67 Query: 61 -INPAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHF-------KASTDE 112 +NPA+ +A L G Y +A+V G + +V+ +Y+ F + Sbjct: 68 HLNPAVTIALWLFGTFERHRVPAYILAQVAGAFCSAALVYGLYSSLFFDFEQAQQMVRGS 127 Query: 113 ISPITIRNLFCTAP-AVRNLPRNFFVELFDTFIFISGILAISE----IKTPGIVPIGVGL 167 + + + ++F T P A + + F VE+ T I ++ I+AI++ + + + P+ +GL Sbjct: 128 VESLELASIFSTYPHASLSFGQAFLVEMVITAILLAMIMAITDDGNGLPSGPLAPLLIGL 187 Query: 168 LVWAIGMGLGGPTGFAMNLARDMGPRIAHAIL---PIANKADSDWQYGIIVPGIAPFVGA 224 L+ IG +G TGFAMN ARD GP++ +A D Y +VP AP +GA Sbjct: 188 LIAVIGGAMGPLTGFAMNPARDFGPKLMTFFAGWGDVAFTGGKDIPY-FLVPIFAPILGA 246 Query: 225 AIAA 228 + A Sbjct: 247 CLGA 250 Lambda K H 0.330 0.145 0.470 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: 263 Number of extensions: 20 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: 238 Length of database: 293 Length adjustment: 25 Effective length of query: 213 Effective length of database: 268 Effective search space: 57084 Effective search space used: 57084 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: 47 (22.7 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