Align High-affinity proline transporter PutP (characterized)
to candidate WP_090274945.1 BLU11_RS15570 sodium/proline symporter PutP
Query= SwissProt::P94392 (473 letters) >NCBI__GCF_900105005.1:WP_090274945.1 Length = 500 Score = 526 bits (1355), Expect = e-154 Identities = 262/468 (55%), Positives = 344/468 (73%), Gaps = 13/468 (2%) Query: 1 MLLIGYFAYKRTSNLTDYMLGGRSLGPAVTALSAGAADMSGWLLMGLPGAMFSTGLSGAW 60 ML IGY+AY++T++L DYML GR L P V ALSAGA+DMSGWLLMGLPGA++++GL AW Sbjct: 18 MLGIGYYAYRQTTDLDDYMLAGRKLSPGVAALSAGASDMSGWLLMGLPGAIYASGLVEAW 77 Query: 61 IVIGLCLGAWANWLYVAPRLRTYTEKAGNSITIPGFLENRFGDQTKLLRLFSGIVILVFF 120 I IGL +GA+ NW +VAPRLR+YTE + NSIT+P F+ENRF D+T+LLR+ SG++ILVFF Sbjct: 78 IAIGLTIGAYLNWRFVAPRLRSYTEVSNNSITVPSFMENRFKDKTRLLRIASGVIILVFF 137 Query: 121 TFYVSSGMVSGGVLFNSILGMDYHTGLWIVTGVVVAYTLFGGFLAVSWTDFVQGIIMFAA 180 TFYVSSGMV+GGV F + Y G+ +V+G+ + YTLFGGFL S TD VQG++M AA Sbjct: 138 TFYVSSGMVAGGVFFEASFNTPYLFGMLLVSGITLTYTLFGGFLGASLTDVVQGLLMLAA 197 Query: 181 LILVPIVTFFHTGGAGDTVAEIRSVDP-----------DMFNIFKGTSVLGIISLFAWGL 229 LI+VP++T GG G+T+ I + D ++ G S+L IIS +WGL Sbjct: 198 LIIVPVLTVIGMGGLGETIDAIHAADAAHNLANPGDELHRTSLLFGGSLLAIISAASWGL 257 Query: 230 GYFGQPHIIVRFMAITSVKEIKRARRIGMGWMILSAVGAVLTGLGGIAYYHQRGMTLKDP 289 GYFGQPHIIVRFMA+ S + K RRIG+GWMIL A GAV TGL G+ Y+H L +P Sbjct: 258 GYFGQPHIIVRFMALRSSADAKAGRRIGIGWMILVASGAVFTGLIGVGYFHTSNEVLDNP 317 Query: 290 ETIFIQLGNILFHPIITGFLISAILAAIMSTISSQLLVTSSSLVEDLYKSMFRRSASDKE 349 ET+F+ L ILFHP++ G +++A+LAAIMST+SSQL+V SS+LVEDLYK +F + + + Sbjct: 318 ETVFLLLSQILFHPLVAGLVLAAVLAAIMSTVSSQLIVCSSALVEDLYK-IFGKDLTALQ 376 Query: 350 LVFLGRLAVLAVSIVALVLAWEKNNTILGLVSYAWAGFGASFGPVVLLSLFWKRMTKWGA 409 V LGRL VL V+++A +LA + + ILGLV++AWAGFGA+FGP++LLSLFW+++T GA Sbjct: 377 QVRLGRLGVLTVAVIAALLAIDPRSNILGLVAFAWAGFGAAFGPIILLSLFWRKLTAMGA 436 Query: 410 LAGMIVGAATVIIWAN-AGLSDFLYEMIPGFAASLLSVFFVSILTQAP 456 LAGMI GA V IW N A L +YE++PGF A + VS+L + P Sbjct: 437 LAGMITGAVVVGIWGNIASLQALMYEIVPGFLACTVVAIVVSLLIKTP 484 Lambda K H 0.327 0.141 0.432 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: 808 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: 473 Length of database: 500 Length adjustment: 34 Effective length of query: 439 Effective length of database: 466 Effective search space: 204574 Effective search space used: 204574 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