Align General amino-acid permease GAP2 (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= SwissProt::A0A1D8PK89 (588 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 242 bits (617), Expect = 3e-68 Identities = 139/397 (35%), Positives = 213/397 (53%), Gaps = 8/397 (2%) Query: 72 TANSPLTRSLKNRHLQMIAIGGSIGTGLFVGSGSSLHTGGPAGLLIAYILIGTMIYCTVM 131 ++++ L + LK RH+ M++I G IG GLFVGSG ++ GPA +L+AY G ++ + Sbjct: 6 SSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPA-VLLAYAAAGALVVLVMR 64 Query: 132 SLGELAVTFPVSGAFVTYNSRFIDPSWGFAMAWNYAMQWLVVLPLELVAAAMTVKYWDAK 191 LGE+AV P +G+F TY R I GF + W Y W++V+PLE AAA + W Sbjct: 65 MLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPN 124 Query: 192 TNSAAFVVIFYVLIVAINFFGVRGYGEAEFIFSAVKVLAVLGFIILGIVLCAGGGPQGGY 251 AF ++ +L+ A N F V+ YGE EF F+ VKV+A++GFI LGI+ G P Sbjct: 125 VAIWAFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLPTSQV 184 Query: 252 IGGKNWYIEGAPFPNGAKGVITVFVNAAFAFAGTELCGLAAAETENPRKSLPKACKQVFW 311 G + + PNG V+ + F+F GTE+ +AAAE++NP + + KA V W Sbjct: 185 SGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIW 244 Query: 312 RITLFYVICLTLVGLLVPWNDERLLGSSSADASASPFVISIRNAGIKGLPSVMNVVIMIA 371 RI LFY++ + +V LVPWND L AS + + GI ++++V+++A Sbjct: 245 RIGLFYLVSIFIVVALVPWNDPIL-------ASVGSYQTVLERMGIPNAKLIVDIVVLVA 297 Query: 372 VLSVGNSSVYGSSRTLAALAASNQAPKIFGYIDKQGRPLVGIIAQLLVGLLCFLAASDKQ 431 V S NS++Y +SR + +L AP + + G P ++ L A Sbjct: 298 VTSCLNSALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVFANYVAP 357 Query: 432 GEVFNWLLALSGLSSIFTWGSINVCLIRFRRALAAQG 468 VF +LLA SG ++ + I + +R R+ A+G Sbjct: 358 AAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARG 394 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: 600 Number of extensions: 29 Number of successful extensions: 3 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: 464 Length adjustment: 35 Effective length of query: 553 Effective length of database: 429 Effective search space: 237237 Effective search space used: 237237 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