Align L-proline uptake porter, PutP (characterized)
to candidate 209017 DVU0088 Sodium/pantothenate symporter
Query= TCDB::Q9I5F5 (506 letters) >MicrobesOnline__882:209017 Length = 495 Score = 159 bits (402), Expect = 2e-43 Identities = 150/497 (30%), Positives = 226/497 (45%), Gaps = 39/497 (7%) Query: 1 MSVNTPTLITFVIYIAAMVLIGLAAYRSTNN-------FSDYILGGRSLGSFVTALSAGA 53 MS T + V+Y+A + L A T +Y +GGRS+G FV A++ A Sbjct: 1 MSAQFMTTVPVVLYLALSFGVALWARGRTAEGGSAKDIIEEYYIGGRSMGGFVLAMTIIA 60 Query: 54 SDMSGWLLMGLPGAVYLSGLSESWIAIGLI-VGAYLNWLFVAGRLRVQTEHNGNALTLPD 112 S S +G PG Y GLS W+ + +I V L V G+ A+TL D Sbjct: 61 SYTSAGSFVGGPGVAYRLGLS--WVLLAMIQVPTTFLTLGVLGKRFAIVARRAGAVTLTD 118 Query: 113 YFTNRFEDNSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATI 172 Y R+ ++ ++ +AL LVFF + + GARLF++ G Y L + Sbjct: 119 YLLARYRSHTVVILCSAAL--LVFFMAAMLAQFIGGARLFQTVTGYPYVVGLALFGVTVV 176 Query: 173 AYTFIGGFLAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDML-K 231 YT +GGF AV TD VQ +M+ A+++ + V+ A GG+ ++ D Sbjct: 177 LYTAVGGFRAVVVTDAVQGIVMVVAVVVVLLAVIDAGGGMTQCIATLKAIDPGLITPTGP 236 Query: 232 GASFIGVISLMAW---GLGYFGQPHILARFMAADSVKSIPAARRIS---MTWMILCLGGA 285 G + L W GLG G P R M +++ A I + +MILC A Sbjct: 237 GDAVPQPFMLSFWVLVGLGVLGLPQTTQRCMGYRDSRAMHDAMIIGTLLIGFMILC---A 293 Query: 286 VAVGFFGIAYFQAHPEQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQ 345 G G A P AG + L L +P+ AGV ++ LAA+MST+ Sbjct: 294 HLAGTLGRAVLPDLP--AG------DLAMPSLIVQLLSPFWAGVFIAGPLAAIMSTVDSM 345 Query: 346 LLVCSSALTEDFYKAFLRKG-ASQLELVWVGRAMVLLVAVIAIWL---ASNPENRVLGLV 401 LL+ S+A+ +D Y + G S+L V + R V AVI + + A P + ++ + Sbjct: 346 LLLASAAIVKDLYVRYRLGGDTSRLRPVTMKRMSVASTAVIGVLVFVAAMEPPDLLVWIN 405 Query: 402 SYAWAGFGAAF-GPLVLFSLLWKRMTRNGALAGMIVGAATVILWKNLL--GWTGLYEIIP 458 +A+ G A F PLVL L W+R GA+A ++ G T +W + G++ I+P Sbjct: 406 LFAFGGLEAVFLWPLVL-GLYWRRGNATGAIASILSG-VTAFVWLTIAKPDMGGIHAIVP 463 Query: 459 GFLFASVAIVVFSLLGK 475 L + V V SL G+ Sbjct: 464 TTLLSLVMFVAGSLAGR 480 Lambda K H 0.326 0.138 0.421 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: 695 Number of extensions: 41 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: 506 Length of database: 495 Length adjustment: 34 Effective length of query: 472 Effective length of database: 461 Effective search space: 217592 Effective search space used: 217592 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: 52 (24.6 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