Align proline porter II (characterized)
to candidate BPHYT_RS08740 BPHYT_RS08740 membrane protein
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS08740 Length = 427 Score = 266 bits (681), Expect = 8e-76 Identities = 145/415 (34%), Positives = 229/415 (55%), Gaps = 19/415 (4%) Query: 22 KLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPL 81 K+ + I AAS+GNA+EWFD VYGF A + K+FFP ++ ++ L TF + ++IRPL Sbjct: 17 KVHRIILAASIGNALEWFDLVVYGFFAVTIAKLFFPARTEAISLMLTLGTFGISYMIRPL 76 Query: 82 GGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSV 141 GGL G L D+ GR+ L ++I +M + T I ++P Y IG+WAP +++ ++ QGFS Sbjct: 77 GGLVLGSLADRAGRKASLLLSIALMMVGTLTIAVMPPYAAIGLWAPAGIMLSRLVQGFSA 136 Query: 142 GGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWR 201 GGE+ ++ F+ E++P+R RGFMGSW +L +G L+++ + A WGWR Sbjct: 137 GGEFGASTAFLVEHAPER-RGFMGSWQFASQGMATLLASGFGALLTSQLTSAQLESWGWR 195 Query: 202 IPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSL 261 +PF L +G +G Y+R ++E F E R L+D T+ R L Sbjct: 196 VPFLFGLAIGPVGFYIRRYVDEGAEF-----NAEPKARTPLRD-------LFGTQKVRML 243 Query: 262 LTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDR 321 L L+I+T Y +L YMP+Y LH G +A + + + P G LSDR Sbjct: 244 LAVGSLIISTAANYMIL--YMPTYAIKQLHLPASTGFAATLATGVVLTVLTPFAGHLSDR 301 Query: 322 FGRRPFVLLGSVALFVLAIPAFILINS--NVIGLIFAGLLMLAVILNCFTGVMASTLPAM 379 GR + +V + V PAF+ +N+ + + ++ A L+ + V+ + G + + + + Sbjct: 302 LGRIRIMATAAVLMLVTVYPAFVYMNAHPSFVTMLLA-LIWIGVLKATYFGALPALMSEI 360 Query: 380 FPTHIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLI 433 FPT R + LA ++NI V V G P + WL+++S N + P +YLM AV L+ Sbjct: 361 FPTQTRATGLAVSYNIGVTVFGGFAPFVITWLIDASGNKLAPGFYLMFCAVASLL 415 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: 575 Number of extensions: 28 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: 427 Length adjustment: 33 Effective length of query: 467 Effective length of database: 394 Effective search space: 183998 Effective search space used: 183998 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