Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 291 bits (746), Expect = 2e-83 Identities = 171/418 (40%), Positives = 237/418 (56%), Gaps = 66/418 (15%) Query: 8 PDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRA 67 P PPPG GV W+R N+FSS N++LTL A LIY ++ + W +L+ W + A Sbjct: 18 PPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSSTLPW-LLNGVWTTNSLA 76 Query: 68 DCT-----KEGACWVFIQQRFGQFMYGY-YPADLRWRVDLTVWLAVIGVAPLFISRFPRK 121 +C K GAC+ + +R+ Q +YG+ YP WR +L + L ++ +AP+ PRK Sbjct: 77 ECREVLDGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVLLLVALAPVLFFDLPRK 136 Query: 122 AIYGLSFLVLYPISAWCLLHG------------------------------GVFG----- 146 L+F +YP A+ L+ G G FG Sbjct: 137 L---LAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGKGSFALGFFGAIVAA 193 Query: 147 --------------------LDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSN 186 L AV + GG ML +++ + ++PLGI LALGR+SN Sbjct: 194 VVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSVPLGIALALGRQSN 253 Query: 187 MPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIA 246 MP I+ +CV FIEF RGVPLIT+LF++SVML F P D LR +I + LF +AYIA Sbjct: 254 MPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRVVIMITLFSAAYIA 313 Query: 247 EVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVI 306 EV+RGGL A+PKGQYEAA ++GL Y ++M L+ILPQALK+ IPGIVN + LFKDT+LV Sbjct: 314 EVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVNVAVGLFKDTTLVS 373 Query: 307 IIGLFDLLNSVK-QAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGH 363 +I +FDL+ ++ A +W G+ E FAA +F+I C+G+S+YS LER+L T H Sbjct: 374 VISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFFIVCYGISQYSQWLERRLATDH 431 Lambda K H 0.330 0.144 0.469 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: 599 Number of extensions: 26 Number of successful extensions: 6 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: 365 Length of database: 432 Length adjustment: 31 Effective length of query: 334 Effective length of database: 401 Effective search space: 133934 Effective search space used: 133934 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 (21.9 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