Align proline porter II (characterized)
to candidate HSERO_RS00050 HSERO_RS00050 membrane protein
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__HerbieS:HSERO_RS00050 Length = 437 Score = 263 bits (672), Expect = 9e-75 Identities = 135/439 (30%), Positives = 239/439 (54%), Gaps = 11/439 (2%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 ++ + AA +GNA+EW+DF VYGF + + ++FFP + ++ ALATF + F +RP+GG Sbjct: 8 QRQVIAAIVGNALEWYDFIVYGFFSAIIARLFFPADNEYTSLLVALATFGIGFFMRPVGG 67 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 + G+ D+ GR+ + + IV+M+++ I P+Y TIGI API++++ +M QGF+ GG Sbjct: 68 VLLGLYADRKGRKAAMQVIIVLMTLAIAIIAFTPTYATIGIAAPIMIVVARMLQGFATGG 127 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 EY+ ++ F+ E +P KRG GSW G GAG+ L++ + WGWR+P Sbjct: 128 EYSSSTAFLVESAPAHKRGLYGSWQLVGQCLAVFCGAGMGALVTRNLSPEALDSWGWRLP 187 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F + L +G +GL++R + ET F + +K + + ++ R +L Sbjct: 188 FVLGLLIGPVGLWIRRHMHETDDFLESANK---------PNAAPIKLLDVVKTNLRGVLV 238 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFG 323 +G VI V +Y++L MP++ + L D ++ + + + V P G LSDR G Sbjct: 239 SMGQVINGTVAFYVVLVNMPTFANKQLGLPLDQAFMVQMIAVALLTAVIPFAGALSDRLG 298 Query: 324 RRPFVLLGSVALFVLAIPAFILIN-SNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPT 382 RR +L S+A ++ P F+ ++ + + + ++L +++ G M + L FPT Sbjct: 299 RRTVLLYSSLAFLLMVYPLFVWVSAAPSLPRLLVMQVLLCIVIGANFGPMPTALSEQFPT 358 Query: 383 HIRYSALAAAFNI-SVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKET 441 +R + LA A+N+ ++L G P + WL ++S + + PA+Y++ A +G+ M++ Sbjct: 359 RVRSTGLAVAYNLAAMLFGGFAPFIVTWLTKTSGSPVAPAWYVLFAACIGVSAAWAMRDQ 418 Query: 442 ANRPLKGATPAASDIQEAK 460 + T + I E K Sbjct: 419 SPAAKNRQTEVFAGIGEIK 437 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: 591 Number of extensions: 35 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: 500 Length of database: 437 Length adjustment: 33 Effective length of query: 467 Effective length of database: 404 Effective search space: 188668 Effective search space used: 188668 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