Align Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel (characterized)
to candidate Pf1N1B4_766 Glycerol uptake facilitator protein
Query= SwissProt::F9UMX3 (238 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_766 Length = 269 Score = 90.5 bits (223), Expect = 3e-23 Identities = 75/248 (30%), Positives = 120/248 (48%), Gaps = 26/248 (10%) Query: 6 LAEFMGTALMIIFGVGVHCSEVLKGTKYRGSGHIFAITTWGFGITIALFIFGNVC---IN 62 +AEF+GTAL+I FG G + + G + G I I WG G+++A+++ V +N Sbjct: 1 MAEFLGTALLIFFGTGCVAALKVAGASF-GLWEISII--WGGGVSMAIYLTAGVSGAHLN 57 Query: 63 PAMVLAQCILGNLSWSLFIPYSVAEVLGGVVGAVIVWIMYAD--------HFAASADEIS 114 PA+ +A I + Y ++V G GA++V+ +Y++ H + S Sbjct: 58 PAVSIALSIFADFEKRKLPFYIFSQVAGAFCGALLVYTLYSNLFFDFEQTHQMVRGTQAS 117 Query: 115 PITIRNLFSTAP-AVRNLPRNFFVEFFDTFIFISGILAISE-----VKTPGIVPIGVGLL 168 + + ++FST P + F VE T I + I+++++ K P + P+ +GLL Sbjct: 118 -LELASVFSTFPNPALTTAQAFLVEVIITAILMGVIMSLTDDNNGLPKGP-LAPLLIGLL 175 Query: 169 VWAIGMGLGGPTGFAMNLARDMGPRIAHAIL---PIKNKADSDWQYGIIVPGIAPFVGAA 225 + IG +G TGFAMN ARD GP++ I D Y ++P AP VGA Sbjct: 176 IAVIGSSMGPLTGFAMNPARDFGPKLMTFFAGWGEISLTGGRDIPY-FLIPIFAPIVGAC 234 Query: 226 CAALFMHG 233 A G Sbjct: 235 LGAAAYRG 242 Lambda K H 0.330 0.146 0.468 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: 203 Number of extensions: 12 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: 238 Length of database: 269 Length adjustment: 24 Effective length of query: 214 Effective length of database: 245 Effective search space: 52430 Effective search space used: 52430 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: 46 (22.3 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