Align Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate BWI76_RS25550 BWI76_RS25550 sodium:pantothenate symporter
Query= SwissProt::O06493 (492 letters) >FitnessBrowser__Koxy:BWI76_RS25550 Length = 483 Score = 187 bits (476), Expect = 5e-52 Identities = 141/484 (29%), Positives = 242/484 (50%), Gaps = 38/484 (7%) Query: 1 MSIEIIISLGIYFIAMLLIGWYAFKKTTD---INDYMLGGRGLGPFVTALSAGAADMSGW 57 M EII+ L +Y + + + YA +K + +++Y LG R +G FV A++ A +S Sbjct: 1 MQFEIIVVLLVYLLVVFGLSIYAMRKRSSGSFLSEYFLGSRSMGGFVLAMTLTATYISAS 60 Query: 58 MLMGVPGAMFATGLS----------TLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAIT 107 +G PGA + GL T+WL+LG+ +G + +LA R +AIT Sbjct: 61 SFIGGPGAAYKYGLGWVLLAMIQVPTIWLSLGI-LG--KKFAILARRY--------NAIT 109 Query: 108 IPDFFDKRFQHSSSLLKIVSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTA 167 + D R+Q S + ++++ +++ F + + G RL E+A G Y+ GL + Sbjct: 110 LNDMLQARYQ--SRAVVWIASVSLLVAFVGAIAVQFIGGARLLETAAGIKYETGLLIFGI 167 Query: 168 VVVLYTLFGGFLAVSLTDFVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDI 227 + LYT FGGF A L D +QG +M +++ + GG+ + ++P L+ Sbjct: 168 TIALYTAFGGFRASVLNDTMQGMVMLIGTIVLLVGVVHAAGGLHNAVDTLQHIDPKLVSP 227 Query: 228 FKGASVISIISYLA--WGL---GYYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLG 282 GA+ I +++ W L G G PH VR ++ KD K + IG + I + G Sbjct: 228 -HGANDILTPAFMTSFWVLVCFGVIGLPHTAVRCISYKDSKAVHRGIIIGTIVVAILMFG 286 Query: 283 SVLTGLIGVAYAHKFGVAVKDPEMIFIIFSKILFHPLITGFLLSAILAAIMSSISSQLLV 342 L G +G A V P+ + + P G L+A +AAIMS++++ LL Sbjct: 287 MHLAGALGRAVLPHLTV----PDQVIPTLMVQVLPPWAAGLFLAAPMAAIMSNVNAHLLQ 342 Query: 343 TASAVTEDLYRSFF-RRKASDKELVMIGRLSVLVIAVIAVLLSLNPNSTILDLVGYAWAG 401 ++ + +DL+ S +K ++++L I ++ LV+ ++ +L + P I+ L A+ G Sbjct: 343 ASATIIKDLWLSAQPTKKHNEQKLKRISTIATLVLGILMMLAAWRPPEMIIWLNLLAFGG 402 Query: 402 FGSAFGPAILLSLYWKRMNEWGALAAMIVGAATVLIWITTGLAKSTGVYEIIPGFILSMI 461 + F ++L LYW+R N GAL+AMIVG I T L + G + I+P +LS++ Sbjct: 403 LEAVFLWPLVLGLYWERANATGALSAMIVGGVLYAILATFNL-QYLGFHPIVPSLLLSLL 461 Query: 462 AGII 465 A ++ Sbjct: 462 AFLV 465 Lambda K H 0.328 0.142 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: 645 Number of extensions: 33 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: 492 Length of database: 483 Length adjustment: 34 Effective length of query: 458 Effective length of database: 449 Effective search space: 205642 Effective search space used: 205642 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 (21.8 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