Align lysine-specific permease (characterized)
to candidate PfGW456L13_375 transport permease protein of gamma-aminobutyrate
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_375 Length = 463 Score = 277 bits (709), Expect = 5e-79 Identities = 152/429 (35%), Positives = 240/429 (55%), Gaps = 12/429 (2%) Query: 5 TKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYF 64 + T + GL + LK RH+TM++I G IG GLFV SG I+ AGP LL+Y G++V Sbjct: 2 SSTQSSNGLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPA-VLLAYAAAGMLVVL 60 Query: 65 LMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWW 124 +M LGE+A P +GSF+TY + GF +GW YW+ W + I ++ AA ++ W Sbjct: 61 VMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAW 120 Query: 125 FPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKG 184 FP W ++ + ++ + N SV+ +GE E+WF+LIKV +I FI++G++ I G G Sbjct: 121 FPGVDIWAFALVITMLLTVTNLFSVKNYGEFEFWFALIKVLAIIGFIVLGLMAIFGFLPG 180 Query: 185 AQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQ 244 +Q +G S+ + G A++G + FSF GTE++ IAA ES++P K I +A Sbjct: 181 SQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGKQISKATNS 240 Query: 245 VFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVI 304 V WRI LFY+ +I I+ ++P+ DP L S+ + V + G+ +A +++ V+ Sbjct: 241 VIWRIGLFYLVSIFIVVALVPWNDPVL-------ASLGSYQTVLERMGIPNAKMIVDIVV 293 Query: 305 LTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSM 364 L AV S NS +Y S+RML++L G AP + + ++ G P A+ +T A L + Sbjct: 294 LVAVTSCLNSALYTSSRMLFSLGKRGDAPAMSTRTNKSGTPYWAVMLSTGAAFLATFANY 353 Query: 365 FGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFA 424 V+ +LL +SG + +L IAIS R R+ + +G I + FP G +A Sbjct: 354 VAPAAVFEFLLASSGAIALLVYLVIAISQLRMRKQRIARGEKI---AFSMWLFP-GLTYA 409 Query: 425 FILCLIITL 433 I+ ++ L Sbjct: 410 VIVFIVAAL 418 Lambda K H 0.327 0.142 0.451 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: 684 Number of extensions: 40 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: 489 Length of database: 463 Length adjustment: 33 Effective length of query: 456 Effective length of database: 430 Effective search space: 196080 Effective search space used: 196080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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