Align General amino-acid permease GAP2 (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= SwissProt::A0A1D8PK89 (588 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 344 bits (882), Expect = 6e-99 Identities = 180/465 (38%), Positives = 272/465 (58%), Gaps = 8/465 (1%) Query: 77 LTRSLKNRHLQMIAIGGSIGTGLFVGSGSSLHTGGPAGLLIAYILIGTMIYCTVMSLGEL 136 L R LK RHL MIAIGG++GTGLFV SG+S+ GP G L+ Y LIG M+YC + SLGEL Sbjct: 18 LQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLGEL 77 Query: 137 AVTFPVSGAFVTYNSRFIDPSWGFAMAWNYAMQWLVVLPLELVAAAMTVKYWDAKTNSAA 196 AV PV+G+FVTY++ +++ +GFA+ W+Y V + +EL AA + ++YW + Sbjct: 78 AVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSGVV 137 Query: 197 FVVIFYVLIVAINFFGVRGYGEAEFIFSAVKVLAVLGFIILGIVLCAG---GGPQGGYIG 253 + F +L+ +N F VRG+GEAE+ F+ +KV +L F+ G+++ G GGPQ G+ Sbjct: 138 WSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQSGW-- 195 Query: 254 GKNWYIEGAPFPNGAKGVITVFVNAAFAFAGTELCGLAAAETENPRKSLPKACKQVFWRI 313 N+ + APF G + V + A F+F GTE G+AA E +P +++P+A +Q FWRI Sbjct: 196 -HNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQTFWRI 254 Query: 314 TLFYVICLTLVGLLVPWNDERLLGSSSADASASPFVISIRNAGIKGLPSVMNVVIMIAVL 373 LFYV+ + ++G+L+P+ D LL + D SPF + R+AG+ +MN V++ A+L Sbjct: 255 LLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVLTALL 314 Query: 374 SVGNSSVYGSSRTLAALAASNQAPKIFGYIDKQGRPLVGIIAQLLVGLLCFLAASDKQGE 433 S G SS+Y S+R L LA S +AP+ + G P V + A VG LCFL++ Sbjct: 315 SAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLFGDKA 374 Query: 434 VFNWLLALSGLSSIFTWGSINVCLIRFRRALAAQGRDTGELVFTSQVGVIGAIWGAFLNT 493 V+ WLL SG++ W I + RFRR L QG +L + S + G ++ L Sbjct: 375 VYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAIVLCV 434 Query: 494 VVLCLQFWIAVWPLHSSPSAEAFFSAYLTVPVVIVFYVGHKLWTK 538 V++ Q + A + Y+ VP+ +V ++G++L K Sbjct: 435 VIVLGQNYQAFSDVRG--RWLEIVGTYIGVPLFLVLWLGYRLVKK 477 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: 775 Number of extensions: 33 Number of successful extensions: 1 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: 588 Length of database: 509 Length adjustment: 36 Effective length of query: 552 Effective length of database: 473 Effective search space: 261096 Effective search space used: 261096 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