Align L-proline uptake porter, PutP (characterized)
to candidate GFF3020 Psest_3078 sodium/proline symporter
Query= TCDB::Q9I5F5 (506 letters) >FitnessBrowser__psRCH2:GFF3020 Length = 494 Score = 762 bits (1968), Expect = 0.0 Identities = 375/492 (76%), Positives = 431/492 (87%), Gaps = 1/492 (0%) Query: 1 MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60 MS++TPTLITF+IYIAAM+LIG AYR+T NF DYILGGRSLGSFVTALSAGASDMSGWL Sbjct: 1 MSISTPTLITFLIYIAAMILIGFVAYRATKNFDDYILGGRSLGSFVTALSAGASDMSGWL 60 Query: 61 LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120 LMGLPGA++++GLSESWIAIGLIVGA+LNWLFVAGRLRV TEHN NALTLPDYF++RFED Sbjct: 61 LMGLPGAIFVAGLSESWIAIGLIVGAWLNWLFVAGRLRVHTEHNHNALTLPDYFSHRFED 120 Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180 SR+LRIFSALVILVFFTIYCASG+VAGARLFES+FG+ YE ALW GAAATI Y FIGGF Sbjct: 121 ESRMLRIFSALVILVFFTIYCASGVVAGARLFESSFGVPYEYALWIGAAATILYVFIGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKGASFIGVIS 240 LAVSWTDTVQA+LMIFAL++TPV V+LA G + I ++ +FDM G SF+ +IS Sbjct: 181 LAVSWTDTVQATLMIFALLITPVFVILALGDMGAAMDTIATQNPAAFDMFSGLSFVAIIS 240 Query: 241 LMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAHP 300 L+AWGLGYFGQPHIL RFMAADS+K+IP ARRI M WMIL L GAVAVGFFGIAYF HP Sbjct: 241 LLAWGLGYFGQPHILVRFMAADSIKTIPNARRIGMAWMILTLAGAVAVGFFGIAYFAGHP 300 Query: 301 EQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKA 360 EQAGAVS+N ERVF+EL KILFNPW+AG++LS +LAAVMSTLS QLLV SSALT+DFYKA Sbjct: 301 EQAGAVSQNGERVFMELVKILFNPWVAGIILSGVLAAVMSTLSAQLLVSSSALTQDFYKA 360 Query: 361 FLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFSL 420 LRK ASQ ELVWVGR MVLL+A+IAI +ASNPE++VLGLVSYAWAGFGAAFGP+VL SL Sbjct: 361 MLRKSASQTELVWVGRGMVLLIALIAIGIASNPESKVLGLVSYAWAGFGAAFGPVVLISL 420 Query: 421 LWKRMTRNGALAGMIVGAATVILWKNLLGWTGLYEIIPGFLFASVAIVVFSLLGKAPSTS 480 LWKRMTRNGALAGM+VGA TV++WK +G GLYEIIPGF+ AS+AI V S +G P+ S Sbjct: 421 LWKRMTRNGALAGMLVGAVTVVVWKEFIG-LGLYEIIPGFILASIAIFVVSKMGAEPAPS 479 Query: 481 MLKRFDDAEQEY 492 ++KRF++A+ +Y Sbjct: 480 IIKRFEEADADY 491 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: 1027 Number of extensions: 48 Number of successful extensions: 2 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: 494 Length adjustment: 34 Effective length of query: 472 Effective length of database: 460 Effective search space: 217120 Effective search space used: 217120 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