Align Amino-acid permease GAP1 (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease
Query= SwissProt::Q5AG77 (582 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139 Length = 501 Score = 226 bits (577), Expect = 1e-63 Identities = 146/434 (33%), Positives = 229/434 (52%), Gaps = 23/434 (5%) Query: 43 DKLT----GVDDIPDRELTDIERININAANSNLQRKLKTRHLQMIAIGSSIGTGLFVGTG 98 D+LT + I + + +N +N L + K RH+ M++I IG GLFVG+G Sbjct: 14 DRLTLSQYALTSITREQKKTMNNLNSRDSNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSG 73 Query: 99 GALSTGGPAAIVLAWAISAISVFMTMQGLGELAVAFPVSGGFNLYASKFLEPGIGFAVGW 158 A++ GPA ++LA+ S + V + M+ LGE+AVA P +G F+ YA + + GF +GW Sbjct: 74 HAIAAAGPA-VLLAYLFSGLLVVLVMRMLGEMAVANPDTGSFSTYADQAIGRWAGFTIGW 132 Query: 159 NYFLQFFVLLPLELVAGAITIKYWNASINSDVFVIIFWFVVLVITMLGVRWYGEAELVFC 218 Y+ + +++P+E +A + W I++ +F + +++V + V YGE E F Sbjct: 133 LYWWFWVLVIPIEALAAGHVLNQWFPQIDTWLFALTSIILLVVTNLFSVSKYGEFEFWFA 192 Query: 219 TIKVIAVIGFIILGIVLICGGGPNHEFIG-GKYWREPGPFA-NSFKGFASSLITAAFSFG 276 KV+A+IGFI LG ++ G P E G + E G FA N + IT FSF Sbjct: 193 MAKVVAIIGFIGLGFAVLMGWIPEREASGLSRLMEEHGGFAPNGLSAVVGAFITIMFSFI 252 Query: 277 GTEMIALTASESSNVRHALPKAIKQVFWRIVIFYLGSIIMIATLVPYNDKRLLGSSSVDV 336 GTE + + A+ESSN + KA + V WRI +FYL SI ++ ++VP+ND L S Sbjct: 253 GTEAVTIAAAESSNPAQNIAKATRSVIWRIGVFYLLSIFVVISVVPWNDPLLASVGS--- 309 Query: 337 TASPFTIAIVNGGIKGLPSVINAVILISVLSVGNASVYATSRTLNSLAEQGMAPKWTGYI 396 + A+ I +++ V+LI+V S N+S+Y SR L SL ++G APK Sbjct: 310 ----YQRALELMNIPHAKLMVDVVVLIAVASCMNSSIYIASRMLFSLGKRGDAPKPLKVT 365 Query: 397 DRAGRPLFAILITNVFG----LFALIAADNEKQVVAFNWLLALSGLSSIFTWMSINLSHI 452 G P A++ + V G LF+ F +LLA SG ++ ++ I +S + Sbjct: 366 SSDGVPRAAVIASTVLGAGVTLFSYFMPAG-----LFQFLLASSGAIALLVYLVIAVSQL 420 Query: 453 RFRRAMKVQNRSLT 466 R R+ + QN +LT Sbjct: 421 RMRKILLRQNVTLT 434 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: 657 Number of extensions: 35 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: 501 Length adjustment: 35 Effective length of query: 547 Effective length of database: 466 Effective search space: 254902 Effective search space used: 254902 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