Align proline porter II (characterized)
to candidate H281DRAFT_04917 H281DRAFT_04917 MFS transporter, MHS family, proline/betaine transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Burk376:H281DRAFT_04917 Length = 433 Score = 277 bits (709), Expect = 5e-79 Identities = 152/417 (36%), Positives = 232/417 (55%), Gaps = 24/417 (5%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 R AI A LGN +EWFDF VY F A + K+FFP + ++ A+ATF V F +RP+GG Sbjct: 21 RHAIIATVLGNGLEWFDFTVYSFFAVIIAKLFFPTGNDLTSLLLAVATFGVGFFMRPVGG 80 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 + G+ DK GR+ L++TI++M+ T IG+ P+Y IG+WAP+L++I ++ QGFS GG Sbjct: 81 IVLGVYADKVGRKAALSLTILLMAGGTALIGIAPTYQQIGLWAPVLIVIARLLQGFSAGG 140 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E A+ F+ EY+P KR + SW+ +LGA V +++ + WGWR+P Sbjct: 141 EMGSATAFLTEYAPANKRAYYSSWIQSSIGFAVLLGAAVGTFVTSSLSTEALHSWGWRMP 200 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F I + +G +G ++R ++ETPAF D E D P E+ ++ R Sbjct: 201 FLIGMLIGPVGYFIRSRMDETPAFSAVAD-------EAKDDSP---LAEVFRRFPRETFA 250 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIG---MLFVQPVMGLLSD 320 +VI V Y+LL YMP+Y LH + G L A M G ++ PV+G L+D Sbjct: 251 SFSMVILWTVCTYVLLFYMPTYSVRTLHLPQSTGFL---AGMFGGSMIMCFAPVVGKLAD 307 Query: 321 RFGRRPFVLLGSVALFVLAIPAFILINSNVIGL----IFAGLLMLAVILNCFTGVMASTL 376 R+GRR F+ +V + VLA P F IN GL +F G + +++ +TG + + Sbjct: 308 RYGRRRFLSGAAVLILVLAWPMFAYIN-RAPGLASLMVFQG--VFGLLIAAYTGPILAAF 364 Query: 377 PAMFPTHIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGL 432 +FPT + + L+ A+N +V + G P WL+ S+ + M PA+Y+M+ A + L Sbjct: 365 SELFPTKVLSTGLSVAYNFAVTIFGGFAPFFITWLIASTGSNMAPAFYVMIAAAISL 421 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: 623 Number of extensions: 36 Number of successful extensions: 6 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: 433 Length adjustment: 33 Effective length of query: 467 Effective length of database: 400 Effective search space: 186800 Effective search space used: 186800 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