Align Amino-acid permease RocE (characterized)
to candidate WP_034528194.1 LOSG293_RS05955 amino acid permease
Query= SwissProt::P39137 (467 letters) >NCBI__GCF_000740055.1:WP_034528194.1 Length = 485 Score = 373 bits (958), Expect = e-108 Identities = 184/478 (38%), Positives = 295/478 (61%), Gaps = 18/478 (3%) Query: 4 NQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLT 63 + +Q++R +K+RH+ MI+LGG IGTG F+ +G I+ AGP GA+++Y G +++ Sbjct: 3 DDQGSHQVKRELKTRHVSMIALGGSIGTGLFVASGSAISTAGPGGALVAYTAMGLMVYFL 62 Query: 64 MLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWF 123 M LGE+A PVSGSF YATK++ PA GFA GW YW WA+T A++ +A +M+ W Sbjct: 63 MTSLGEMATYMPVSGSFAAYATKYVDPAMGFAMGWNYWFNWAITLAVDISTAALVMKFWL 122 Query: 124 PHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLK 183 P I WIW ++ ++F+LNA+T KAF ESE+W + IK++ + +F+ +G A +FG++ Sbjct: 123 PDIPGWIWSVLVLVIIFMLNALTVKAFGESEYWMAMIKVVTVFIFLAVGVATIFGIM--- 179 Query: 184 GGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIK 243 GG ++ F GI +L + F+FQGTEL+G+ AGES+DPEK+IP++I Sbjct: 180 GGHATGLENFTRKEAPFVGGIPTILSVFVVAGFSFQGTELVGITAGESKDPEKSIPKAIN 239 Query: 244 QTVWRTLVFFVLSIIVIAGMIPW--------KQAGVVESPFVAVFEQIGIPYAADIMNFV 295 Q WR ++F++LSI VIA +IP+ + + SPF VF++ G+ AA +MN V Sbjct: 240 QVFWRIILFYILSIFVIACIIPYTSPQLLGSSASDIAISPFTLVFQRAGLAAAASVMNAV 299 Query: 296 ILIALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTK 355 IL +++S ANSG+YAS+R+LY++A +G A KA KT + GVP+ + I+T V L+ + Sbjct: 300 ILTSVISAANSGMYASSRMLYSLAVQGYASKAFTKTTRTGVPLNAQIMTTVVGALTFIAS 359 Query: 356 FAQAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLI 415 A +Y+ L++ +G++ + W+ I+LS FRR +I++G I +LK+ L+P+ P+ Sbjct: 360 IA-GPKIYIWLVAASGLTGFIAWLGIALSHFRFRRAFIKQGHHISELKYHAKLFPIGPIF 418 Query: 416 GLTLNTVVLISLAFDP------EQRIALYCGVPFMIICYIIYHVVIKKRQQANRQLEL 467 L L ++++ D +Q Y VP I Y Y + + + + +++L Sbjct: 419 ALILCLLIIVGQDLDAFTNFNWQQISITYLSVPIFIGLYSYYKIRYRTKLISLEKIDL 476 Lambda K H 0.329 0.142 0.438 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: 568 Number of extensions: 33 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: 467 Length of database: 485 Length adjustment: 33 Effective length of query: 434 Effective length of database: 452 Effective search space: 196168 Effective search space used: 196168 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 (21.8 bits) S2: 51 (24.3 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