Align L-proline uptake porter, PutP (characterized)
to candidate WP_086510759.1 BZY95_RS15245 sodium/proline symporter PutP
Query= TCDB::Q9I5F5 (506 letters) >NCBI__GCF_002151265.1:WP_086510759.1 Length = 492 Score = 506 bits (1302), Expect = e-148 Identities = 260/488 (53%), Positives = 336/488 (68%), Gaps = 14/488 (2%) Query: 10 TFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWLLMGLPGAVY 69 TFV+Y+ M+ IG+ AY+ T N SDYILGGRSLG + +A+SAGASDMSGWLL+GLPGA Y Sbjct: 11 TFVVYLLLMLGIGIVAYKRTTNLSDYILGGRSLGPWTSAISAGASDMSGWLLLGLPGAAY 70 Query: 70 LSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFEDNSRLLRIFS 129 +SG+S SWIA+GL++G +LNWL VA RLR+ + +ALTLP+YF NRF D S+LLR+ S Sbjct: 71 VSGISASWIAVGLLIGTWLNWLIVARRLRLYSFKVSDALTLPEYFANRFRDKSQLLRVIS 130 Query: 130 ALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGFLAVSWTDTV 189 A+ IL+FF Y +SG+VAG RLFE+ FG Y A+ G A I+YTF GGFLAVSWTD + Sbjct: 131 AIFILLFFLFYTSSGLVAGGRLFETVFGYDYTLAVTIGTIAVISYTFFGGFLAVSWTDLI 190 Query: 190 QASLMIFALILTPVIVMLATGGVEPTFTAIELKDATSFDMLKGAS------FIGVISLMA 243 Q +M AL + P+I GG A+ + A + AS FIG++S +A Sbjct: 191 QGLMMAAALAIVPIIAFGDLGGTAGAAAALADESAYMLAWFRDASTGEALTFIGIVSSLA 250 Query: 244 WGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGIAYFQAHPEQA 303 WGLGYFGQPHILARF A S + IPAARRI++TW + L +VAVG G+ + Q Sbjct: 251 WGLGYFGQPHILARFAAIRSDRDIPAARRIAVTWTAIALISSVAVGLLGVGFVQRD---- 306 Query: 304 GAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFLR 363 + E VF+ + ++F+P IAG+LL+AILAA+MST QLLV SSALT+DFYKA R Sbjct: 307 ---LADGETVFMVMVNLIFHPVIAGILLAAILAAIMSTADSQLLVSSSALTDDFYKAIFR 363 Query: 364 KGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFGPLVLFSLLWK 423 K ASQ ELVWVGR V+ +A++A LA NP+ VL LV+YAWAGFGAAFGP ++ SL W+ Sbjct: 364 KDASQAELVWVGRFAVIAIAIVAYLLALNPDATVLDLVAYAWAGFGAAFGPALIMSLYWR 423 Query: 424 RMTRNGALAGMIVGAATVILWKNLLGWT-GLYEIIPGFLFASVAIVVFSLLGKAPSTSML 482 RM + GALAG++ G TV++W L G LYEI+PG + A +AIVV SL + P + Sbjct: 424 RMNKWGALAGIVTGGVTVVVWAELSGGIFDLYEIVPGVILAYIAIVVASLATEEPDLRVT 483 Query: 483 KRFDDAEQ 490 FD ++ Sbjct: 484 ADFDTFDE 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: 863 Number of extensions: 38 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: 506 Length of database: 492 Length adjustment: 34 Effective length of query: 472 Effective length of database: 458 Effective search space: 216176 Effective search space used: 216176 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