Align uncharacterized amino-acid permease C869.11 (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate
Query= CharProtDB::CH_091412 (580 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639 Length = 464 Score = 207 bits (528), Expect = 6e-58 Identities = 131/400 (32%), Positives = 199/400 (49%), Gaps = 16/400 (4%) Query: 73 LKRSLKSRHMQMISIGGAIGTGLYVGSGSSLADGGPASVIINYSLIGIMMFFIVYALGEM 132 L++ LK RH+ M+SI G IG GL+VGSG ++A GPA V++ Y+ G ++ ++ LGEM Sbjct: 11 LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPA-VLLAYAAAGALVVLVMRMLGEM 69 Query: 133 AVAYPVAGGFNTYATRFIDPAWGFAVSWNYFINYFVTFPLELTTCAITFRYWTDINSAAW 192 AVA P G F+TYA R I GF + W Y+ + + PLE A W N A W Sbjct: 70 AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFP-NVAIW 128 Query: 193 ISIFLVVIIIV--NLFGVRAYGEVEFILSTVKVVATFGFIILAIIINCGGVPTDHRGYIG 250 ++ +++ NLF V+ YGE EF + VKV+A GFI L I+ G +PT + Sbjct: 129 AFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLPTSQVSGVS 188 Query: 251 GSIIKHKPFRHGFKGFCSVFTTAAFSFSGTEVIGLAAAEVDNPQKALPHAVKQVFWRIAI 310 +G T FSF GTE++ +AAAE NP + + A V WRI + Sbjct: 189 HLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGL 248 Query: 311 FYVVSLILIGLLISPDDPNLMGNGSTSVSPFVLAIKEANIKGLPSVFNAVIIISVVSVTN 370 FY+VS+ ++ L+ +DP L SV + ++ I + + V++++V S N Sbjct: 249 FYLVSIFIVVALVPWNDPIL-----ASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLN 303 Query: 371 SSTYTAGRTLHGMANLKQAPSFFKYTDRLGRPLLAMIVVLLFGFFAYINEADKNGNDVSD 430 S+ YTA R + + AP+ + T+ G P A+++ F A N V+ Sbjct: 304 SALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVF------ANYVAP 357 Query: 431 -TVFNWLLALSGLSNFFTWGSICLCHIIFRLAFKKQGHSL 469 VF +LLA SG + I + + R +G + Sbjct: 358 AAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARGEKI 397 Lambda K H 0.325 0.141 0.429 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: 558 Number of extensions: 23 Number of successful extensions: 5 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: 580 Length of database: 464 Length adjustment: 35 Effective length of query: 545 Effective length of database: 429 Effective search space: 233805 Effective search space used: 233805 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