Align L-proline uptake porter, PutP (characterized)
to candidate WP_040664283.1 ON16_RS13915 sodium/proline symporter
Query= TCDB::Q9I5F5 (506 letters) >NCBI__GCF_000307265.1:WP_040664283.1 Length = 509 Score = 372 bits (956), Expect = e-107 Identities = 207/511 (40%), Positives = 301/511 (58%), Gaps = 29/511 (5%) Query: 2 SVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWLL 61 S N +IT ++Y+ +V IG+A R D+ LGGR LG VTA+SA ASDMS WLL Sbjct: 3 SANICIVITILVYLIVVVGIGVACSRRNRTTDDFYLGGRKLGPLVTAMSAEASDMSSWLL 62 Query: 62 MGLPGAVYLSGLSES-WIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120 MGLPG YLSG++++ W AIGL G YLNWL VA R+R+ T H A+T+P++F+ RF D Sbjct: 63 MGLPGVAYLSGVADAGWTAIGLAAGTYLNWLIVARRIRLYT-HRVGAITIPEFFSKRFGD 121 Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180 R+L +A+VIL+FF Y ASG A +LF S FG+ Y A+ +AYT +GGF Sbjct: 122 ERRILTGIAAVVILIFFIPYTASGFAACGKLFNSLFGIDYVGAMVVSGIIIVAYTTLGGF 181 Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVE---------PTFTAIELKDATSFDMLK 231 LA S TD +Q+ +M AL + + + A GG++ P + ++ L + + Sbjct: 182 LAASTTDFIQSIVMTIALFVMVLFGIRAAGGLDVVMDNARALPGYLSMTLSHDMAANAAN 241 Query: 232 GASFIGVISLMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFF 291 FI ++S +AWGLGYFG PHIL RFMA + + + +RR++ W+++ + A+ +G Sbjct: 242 PYGFITIVSTLAWGLGYFGMPHILLRFMAIEDERKLKLSRRVASIWVVISMAVAIFIGIV 301 Query: 292 GIAYFQAHPEQAGAVS----ENPERVFIELAKILFNPWI-----AGVLLSAILAAVMSTL 342 G +AG + E V + LA +L I AGV+L+ ILA+ MST Sbjct: 302 GYGV-----TKAGGIGFLEGSASETVIVRLAGLLSTYGIPAALLAGVVLAGILASTMSTS 356 Query: 343 SCQLLVCSSALTEDFYKAFLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVS 402 QLL +S+++++ + ++ + V R V+ +A+IA+++A NP + V G+VS Sbjct: 357 DSQLLAAASSVSQNLMSECFQVKMNEKKKVTAARLTVVGIALIAMFMARNPNSSVFGIVS 416 Query: 403 YAWAGFGAAFGPLVLFSLLWKRMTRNGALAGMIVGAATVILWKNLL----GWTGLYEIIP 458 +AWAGFGAAFGP+VLF L WKR GALAGM+ G + +WK L+ G +YE++P Sbjct: 417 FAWAGFGAAFGPVVLFGLFWKRTNWQGALAGMVSGGVMIFVWKYLVRPLGGVWNIYELLP 476 Query: 459 GFLFASVAIVVFSLLGKAPSTSMLKRFDDAE 489 FL A V IV SL AP ++ F+D + Sbjct: 477 AFLVACVFIVAVSLATTAPKQEIVDTFNDVK 507 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: 765 Number of extensions: 43 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 472 Effective length of database: 475 Effective search space: 224200 Effective search space used: 224200 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 24 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