Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 287 bits (734), Expect = 4e-82 Identities = 168/427 (39%), Positives = 245/427 (57%), Gaps = 63/427 (14%) Query: 7 SFVRASMIEASPAPSLESGAVSWLRKNLFATPKDTALTIISLLILAWLVPPAIQWLFIDA 66 +FVR + I +P P E+G W+R+NLF++ ++ LT+ +L ++ L+ + WL ++ Sbjct: 10 AFVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSSTLPWL-LNG 68 Query: 67 AWSGGGRGVCATLSQGGSQPEGWSGACWAFVNAKFAQFLFG-RYPLDERWRPALVGILFV 125 W+ C + +G GAC++ + ++ Q L+G +YP E WRP L +L + Sbjct: 69 VWTTNSLAECREVL------DGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVLLL 122 Query: 126 LLLVPMLIPRIPYKGLNALLL--------------LVALPILSAILLPG----------- 160 + L P+L +P K L + LV + L + G Sbjct: 123 VALAPVLFFDLPRKLLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGKGSF 182 Query: 161 --GWFGLTYVETPLW-------------------------GGLMVTLVLSFVGIAVSLPL 193 G+FG +W GG M+ ++L +++S+PL Sbjct: 183 ALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSVPL 242 Query: 194 GILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMASVMLPLFLPQGVTFDKFLRALI 253 GI LALGR+SNMP+IK +C VFIE +RGVPLIT+LF+ASVML F P T D FLR +I Sbjct: 243 GIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRVVI 302 Query: 254 GVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTF 313 ++LF++AY+AEV+RGGL A+PKGQYE ADSLGL + Q M I+LPQALK+ IPGIVN Sbjct: 303 MITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVNVA 362 Query: 314 IGLFKDTSLVSIIGMFDLLGIVR-LNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYS 372 +GLFKDT+LVS+I MFDL+G++R + T W L G FA F+F++ C+G+S+YS Sbjct: 363 VGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLG--FAAFLFFIVCYGISQYS 420 Query: 373 GFMERLL 379 ++ER L Sbjct: 421 QWLERRL 427 Lambda K H 0.329 0.144 0.454 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: 546 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 384 Length of database: 432 Length adjustment: 31 Effective length of query: 353 Effective length of database: 401 Effective search space: 141553 Effective search space used: 141553 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 (21.8 bits) S2: 50 (23.9 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