Align L-proline uptake porter, PutP (characterized)
to candidate 5209987 Shew_2435 sodium/proline symporter (RefSeq)
Query= TCDB::Q9I5F5 (506 letters) >FitnessBrowser__PV4:5209987 Length = 483 Score = 521 bits (1343), Expect = e-152 Identities = 271/493 (54%), Positives = 345/493 (69%), Gaps = 13/493 (2%) Query: 1 MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60 M++ P L+TF Y+ M+ IGL AY++T++ DYILGGRS+G VTALS GASDMSGWL Sbjct: 1 MNIELPILVTFFGYLILMMGIGLWAYKATDSVDDYILGGRSMGPAVTALSVGASDMSGWL 60 Query: 61 LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120 L+GLPGAVYL GL E+WI IGL+ GA+LNWLFVA RLR+ T+ NALTLPD+F RFED Sbjct: 61 LLGLPGAVYLGGLGEAWIGIGLVFGAWLNWLFVAKRLRIYTQFTDNALTLPDFFEKRFED 120 Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180 +L++ SA+ ILVFFT Y +SG+V GA LFE FGL Y AL G+ +AYTF+GGF Sbjct: 121 KQSVLKLVSAVTILVFFTFYTSSGMVGGAILFEKVFGLDYNLALLIGSGIIVAYTFVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLK-GASFIGVI 239 AVSWTD Q LM+ AL++ PV + T I D +L + IG+ Sbjct: 181 FAVSWTDFFQGCLMLIALLIVPVTIF----SQPETQNGIHSLDPAMLSLLSDNTTMIGLA 236 Query: 240 SLMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAH 299 SL+AWGLGYFGQPHIL+RFMA S + +RRI+M+WMI+ L GA+A G G YF Sbjct: 237 SLLAWGLGYFGQPHILSRFMAIGSADDLKVSRRIAMSWMIVALMGALATGLAGTLYFADQ 296 Query: 300 PEQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYK 359 P +NPE +FI LA FNPWI G+L++AIL+A+MST+ QLLVCSS +TEDFYK Sbjct: 297 P------IDNPETIFIHLAHAAFNPWIGGLLVAAILSAIMSTIDSQLLVCSSVITEDFYK 350 Query: 360 AFLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFS 419 +LR AS EL+ +GR VL +AVI+ +A NPE+ VL LVSYAWAGFGAAFGP+V+ S Sbjct: 351 KWLRPDASSKELMMIGRIGVLTIAVISGVIALNPESSVLSLVSYAWAGFGAAFGPVVILS 410 Query: 420 LLWKRMTRNGALAGMIVGAATVILWKNLLGWT-GLYEIIPGFLFASVAIVVFSLLGKAPS 478 L W+ +RNGA+A +IVGA TV+LWK G LYEI+PGFLFA++A V+ SL+ AP+ Sbjct: 411 LFWRGYSRNGAVATIIVGAITVVLWKQSTGGIFDLYEILPGFLFATLAGVLVSLV-SAPA 469 Query: 479 TSMLKRFDDAEQE 491 S ++F+ Q+ Sbjct: 470 DSTREQFEQFSQK 482 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: 871 Number of extensions: 39 Number of successful extensions: 5 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: 483 Length adjustment: 34 Effective length of query: 472 Effective length of database: 449 Effective search space: 211928 Effective search space used: 211928 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