Align Amino-acid permease GAP1 (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP
Query= SwissProt::Q5AG77 (582 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Length = 473 Score = 244 bits (623), Expect = 6e-69 Identities = 151/443 (34%), Positives = 237/443 (53%), Gaps = 11/443 (2%) Query: 65 NAANSNLQRKLKTRHLQMIAIGSSIGTGLFVGTGGALSTGGPAAIVLAWAISAISVFMTM 124 N+ + L+R LK RH+Q+IA+G +IGTGLF+G+ G L + GP+ ++L +AI FM M Sbjct: 5 NSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAICGFIAFMIM 63 Query: 125 QGLGELAVAFPVSGGFNLYASKFLEPGIGFAVGWNYFLQFFVLLPLELVAGAITIKYWNA 184 + LGE+ V PV+G F+ +A K+ GF GWN ++ + ++ EL A I YW Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP 123 Query: 185 SINSDVFVIIFWFVVLVITMLGVRWYGEAELVFCTIKVIAVIGFIILGIVLICGGGPNHE 244 I + V F+ ++ +I + V+ +GEAE F IKV+A++G I LG L+ G + Sbjct: 124 DIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDGGPQ 183 Query: 245 FIGGKYWREPGPFANSFKGFASSLITAAFSFGGTEMIALTASESSNVRHALPKAIKQVFW 304 W G F N G ++ FSFGG EM+ TA+E+ + +PKAI QV + Sbjct: 184 ASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIY 243 Query: 305 RIVIFYLGSIIMIATLVPYND-KRLLGSSSVDVTASPFTIAIVNGGIKGLPSVINAVILI 363 RI+IFY+G+++++ +L P++ L +S + SPF G ++N V+L Sbjct: 244 RILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLT 303 Query: 364 SVLSVGNASVYATSRTLNSLAEQGMAPKWTGYIDRAGRPLFAILITNVFGLFALIAADNE 423 + LSV N+ Y SR L +AEQG APK ID+ G P+ +IL + L A++ Sbjct: 304 AALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLNYLV 363 Query: 424 KQVVAFNWLLALSGLSSIFTWMSINLSHIRFRRAMKVQNRSLTELPFVAQSGVWGSYFGL 483 Q A L++L + + W I+ SH +FR+ M N++ F A +G+Y L Sbjct: 364 PQ-HALELLMSLVVATLVINWAMISFSHFKFRQHM---NKTKQTPLFKALWYPYGNYVCL 419 Query: 484 T-----LNILYLIAQFYIGLFPV 501 L ++ LI I ++ + Sbjct: 420 AFVVFILGVMLLIPGIQISVYAI 442 Lambda K H 0.325 0.140 0.430 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: 701 Number of extensions: 40 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: 582 Length of database: 473 Length adjustment: 35 Effective length of query: 547 Effective length of database: 438 Effective search space: 239586 Effective search space used: 239586 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 (21.6 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