Align proline porter II (characterized)
to candidate WP_083763475.1 AMB_RS08370 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >NCBI__GCF_000009985.1:WP_083763475.1 Length = 445 Score = 212 bits (540), Expect = 2e-59 Identities = 130/422 (30%), Positives = 215/422 (50%), Gaps = 21/422 (4%) Query: 31 SLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGGLFFGMLG 90 S+GN +E++D+ VY + K FFPG DP+VQ++ A F++ F +RPLGG G Sbjct: 35 SVGNLVEYYDWYVYSAFSLYFSKYFFPGDDPTVQLLNTSAIFALGFFMRPLGGWLLGTHA 94 Query: 91 DKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGGEYTGASI 150 D+ GR+ L +++ +M + I ++P Y++IG+ API L++ ++ QG S+GGEY A+ Sbjct: 95 DRKGRKAALLVSVSMMCAGSLIIAVMPGYNSIGVAAPIALILARLLQGLSLGGEYGSAAT 154 Query: 151 FVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTI-VGEANFLDWGWRIPFFIALP 209 +++E + +RGF S+ I G +L GV++ + + + A WGWRIPF I Sbjct: 155 YLSEIATKDRRGFYSSFQYVTLIMGQLLALGVLMALQRVFLTTAELEAWGWRIPFVIGGL 214 Query: 210 LGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLTCIGLVI 269 I+ +YLR ++EET +F+ H +GDR G S ++ R +LT IGL + Sbjct: 215 CAIVAIYLRSSMEETESFEHH-----KGDRVG------ESRIRALMRHPREVLTVIGLTM 263 Query: 270 ATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFGRRPFVL 329 V +Y TYM YL + +S+ +I A + + P++G +SD+ GRR ++ Sbjct: 264 GGTVAFYTFTTYMQKYLVNTAGFSKSDATMISAAATFVYMLMHPLVGHISDKVGRRAVLI 323 Query: 330 LGSVALFVLAIPAFILINS-----NVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTHI 384 V + +P + L+ +GL I++ ++ + A +FP I Sbjct: 324 AFGVMSTLCTVPILTALGQTHDSVTAFFLVLSGL----TIVSGYSAINAVVKAELFPVQI 379 Query: 385 RYSALAAAFNISVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKETANR 444 R + F I V + G T A +S N +Y+ + GL+ V MK+T Sbjct: 380 RALGVGLPFAIGVSLFGGTAEYIALWFKSMGNETWFYWYVTGCCLCGLLLFVGMKDTKKT 439 Query: 445 PL 446 L Sbjct: 440 SL 441 Lambda K H 0.327 0.142 0.429 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: 564 Number of extensions: 29 Number of successful extensions: 5 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: 500 Length of database: 445 Length adjustment: 33 Effective length of query: 467 Effective length of database: 412 Effective search space: 192404 Effective search space used: 192404 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 (21.7 bits) S2: 51 (24.3 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