Align Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel (characterized)
to candidate CA265_RS07865 CA265_RS07865 aquaporin
Query= SwissProt::F9UMX3 (238 letters) >FitnessBrowser__Pedo557:CA265_RS07865 Length = 246 Score = 168 bits (425), Expect = 1e-46 Identities = 96/242 (39%), Positives = 135/242 (55%), Gaps = 25/242 (10%) Query: 6 LAEFMGTALMIIFGVGVHCSEVLKGTKYRGSGHIFAITTWGFGITIALFIFG---NVCIN 62 LAEF+GTALMI+ G GV + VLKGTK SG I T W + + + + G +N Sbjct: 5 LAEFIGTALMILLGNGVVANVVLKGTKGNNSGWIVITTAWALAVFVGVVVAGPYSGAHLN 64 Query: 63 PAMVLAQCILGNLSWSLFIPYSVAEVLGGVVGAVIVWIMYADHFAASADE---ISPITIR 119 P + L I SW+L Y +A++ G + G+ +VW++Y DHF A+ D+ +P Sbjct: 65 PIVTLGLAIGKGFSWALAPFYIIAQLAGAMTGSFLVWLIYKDHFDATDDQGLKAAP---- 120 Query: 120 NLFSTAPAVRNLPRNFFVEFFDTFIFISGILAISEV----KTPGIVPIGVG--------L 167 F+TAPA+RN+ N E TF+ I I ++ K PIG+G Sbjct: 121 --FATAPAIRNISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAF 178 Query: 168 LVWAIGMGLGGPTGFAMNLARDMGPRIAHAILPIKNKADSDWQYGIIVPGIAPFVGAACA 227 LVW IG+ LGG TG+A+N ARD+GPRI H ++P+K K SDW Y VP + P +G+ A Sbjct: 179 LVWVIGLALGGTTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYA-WVPIVGPIIGSVLA 237 Query: 228 AL 229 A+ Sbjct: 238 AV 239 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: 223 Number of extensions: 13 Number of successful extensions: 4 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: 246 Length adjustment: 23 Effective length of query: 215 Effective length of database: 223 Effective search space: 47945 Effective search space used: 47945 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