Align General amino-acid permease GAP2 (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE
Query= SwissProt::A0A1D8PK89 (588 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211 Length = 474 Score = 281 bits (718), Expect = 6e-80 Identities = 151/400 (37%), Positives = 233/400 (58%), Gaps = 13/400 (3%) Query: 77 LTRSLKNRHLQMIAIGGSIGTGLFVGSGSSLHTGGPAGLLIAYILIGTMIYCTVMSLGEL 136 LTR+LK+RH+ M+++GG IGTGLF+GSG +++ GGP G ++AY++ G ++Y ++ LGEL Sbjct: 16 LTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGFLMYLVMVCLGEL 75 Query: 137 AVTFPVSGAFVTYNSRFIDPSWGFAMAWNYAMQWLVVLPLELVAAAMTVKYWDAKTNSAA 196 +V PVSG+F T+ +++I P+ GF + W Y M W + LE AA M + W + Sbjct: 76 SVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIWY 135 Query: 197 FVVIFYVLIVAINFFGVRGYGEAEFIFSAVKVLAVLGFIILGIVLCAGGGP--QGGYIGG 254 + +F V++ IN R +GEAE+ FS +KV A+LGFI++G+++ G P G Sbjct: 136 WSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGVMPLSSGAPAPM 195 Query: 255 KNWYIEGAPFPNGAKGVITVFVNAAFAFAGTELCGLAAAETENPRKSLPKACKQVFWRIT 314 I + FPNG V V + +AF G E+ G+AA ET+ P KS+P+A + V +R+ Sbjct: 196 ATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVFRVL 255 Query: 315 LFYVICLTLVGLLVPWNDERLLGSSSADASASPFVISIRNAGIKGLPSVMNVVIMIAVLS 374 +FYV+ + ++ +VPW L+ SPFV GI +MN VI+ A+LS Sbjct: 256 IFYVLAIIVLSAIVPWQQAGLM--------ESPFVQVFDMVGIPYAADLMNFVILTAILS 307 Query: 375 VGNSSVYGSSRTLAALAASNQAPKIFGYIDKQGRPLVGIIAQLLVGLLCFLAASDKQGEV 434 VGNS +Y S+R L A++ + APK + K+G PL + L L+ + + + Sbjct: 308 VGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFVAADTL 367 Query: 435 FNWLLALSGLSSIFTWGSINVCLIRFRRALAAQGRDTGEL 474 F L+A+SG+S TW I + +FR+A RD G+L Sbjct: 368 FMVLMAVSGMSGTVTWIVIALAQYKFRKAYL---RDGGKL 404 Lambda K H 0.324 0.139 0.431 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: 754 Number of extensions: 45 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 588 Length of database: 474 Length adjustment: 35 Effective length of query: 553 Effective length of database: 439 Effective search space: 242767 Effective search space used: 242767 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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