Align Amino-acid permease GAP1 (characterized)
to candidate AO356_28340 AO356_28340 GABA permease
Query= SwissProt::Q5AG77 (582 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28340 Length = 466 Score = 229 bits (583), Expect = 2e-64 Identities = 144/410 (35%), Positives = 221/410 (53%), Gaps = 22/410 (5%) Query: 67 ANSNLQRKLKTRHLQMIAIGSSIGTGLFVGTGGALSTGGPAAIVLAWAISAISVFMTMQG 126 +N +L + K RH+ M++I IG GLFVG+G A++ GPA ++LA+ S + V + M+ Sbjct: 9 SNGHLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPA-VMLAYLFSGLLVVLVMRM 67 Query: 127 LGELAVAFPVSGGFNLYASKFLEPGIGFAVGWNYFLQFFVLLPLELVAGAITIKYWNASI 186 LGE+AVA P +G F+ YA + + GF +GW Y+ + +++P+E +A + W ++ Sbjct: 68 LGEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAV 127 Query: 187 NSDVFVIIFWFVVLVITMLGVRWYGEAELVFCTIKVIAVIGFIILGIVLICGGGPNHEFI 246 ++ +F + ++ V + V YGE E F KV+A+IGFI LG ++ G P E Sbjct: 128 DAWLFASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVLMGWIPEREAS 187 Query: 247 G-GKYWREPGPFA-NSFKGFASSLITAAFSFGGTEMIALTASESSNVRHALPKAIKQVFW 304 G + E G FA N + IT FSF GTE + + A+ES N + KA + V W Sbjct: 188 GLSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIW 247 Query: 305 RIVIFYLGSIIMIATLVPYNDKRLLGSSSVDVTASPFTIAIVNGGIKGLPSVINAVILIS 364 RI +FYL SI ++ ++VP+ND L S + A+ I +++ V+LI+ Sbjct: 248 RIGVFYLLSIFVVISVVPWNDPLLASVGS-------YQRALELMNIPHAKFLVDMVVLIA 300 Query: 365 VLSVGNASVYATSRTLNSLAEQGMAPKWTGYIDRAGRPLFAILITNVFG----LFALIAA 420 V S N+S+Y SR L SL +G APK AG P A++ + V G LF+ Sbjct: 301 VASCMNSSIYIASRMLYSLGRRGDAPKALKVTSSAGVPRSAVIASTVLGAGVTLFSYFMP 360 Query: 421 DNEKQVVAFNWLLALSGLSSIFTWMSINLSHIRFRRAMKVQNRSLTELPF 470 F +LLA SG ++ ++ I +S +R RR M+ QN ELPF Sbjct: 361 AG-----LFQFLLASSGAIALLVYLVIAISQLRMRRMMQRQN---IELPF 402 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: 639 Number of extensions: 34 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: 466 Length adjustment: 35 Effective length of query: 547 Effective length of database: 431 Effective search space: 235757 Effective search space used: 235757 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