Align Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel (characterized)
to candidate NP_347406.1 CA_C0770 glycerol uptake facilitator permease
Query= SwissProt::F9UMX3 (238 letters) >NCBI__GCF_000008765.1:NP_347406.1 Length = 242 Score = 147 bits (372), Expect = 1e-40 Identities = 86/239 (35%), Positives = 132/239 (55%), Gaps = 11/239 (4%) Query: 4 QLLAEFMGTALMIIFGVGVHCSEVLKGTKYRGSGHIFAITTWGFGITIALFIFGNVC--- 60 +L+ E +GTA++++FG G + LKGTK +G I +G G+ + +F + Sbjct: 8 KLVCEMLGTAILVLFGNGAVANVELKGTKGYRNGWIIIAIGYGVGVMLPALMFNKISGSQ 67 Query: 61 INPAMVLAQCILGNLSWSLFIPYSVAEVLGGVVGAVIVWIMYADHFAASADEISPITIRN 120 NPAM + + G WS IPY +A+ +G ++G VI++ +Y + + D S I Sbjct: 68 TNPAMTIGLAVNGLFPWSEVIPYILAQFVGAIIGQVILYFIYLPFYKQTEDTKS---ILG 124 Query: 121 LFSTAPAVRNLPRNFFVEFFDTFIFISG---ILAISEVK-TPGIVPIGVGLLVWAIGMGL 176 ST A + F EFF TF+ + G IL + VK TP + +G+G LV ++ L Sbjct: 125 TCSTISASGSHINGFVTEFFGTFLLVLGAMFILNSTGVKSTPAVGYVGLGFLVCSLVASL 184 Query: 177 GGPTGFAMNLARDMGPRIAHAILPIKNKADSDWQYGIIVPGIAPFVGAACAALFMHGFF 235 GGPTG +N ARD+GPRI H++LP+KNK +S+W Y I P +AP G+ A + + Sbjct: 185 GGPTGPGLNPARDLGPRIVHSLLPLKNKGNSEWTYAWI-PVLAPMFGSIIAIFLFNKIY 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: 209 Number of extensions: 11 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: 242 Length adjustment: 23 Effective length of query: 215 Effective length of database: 219 Effective search space: 47085 Effective search space used: 47085 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 24 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