Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate HSERO_RS19250 HSERO_RS19250 glutamate ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__HerbieS:HSERO_RS19250 Length = 249 Score = 80.1 bits (196), Expect = 6e-20 Identities = 72/232 (31%), Positives = 118/232 (50%), Gaps = 21/232 (9%) Query: 141 NFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLMTRWANKRFEATGEPFHKFW 200 N+G + +S G+ L+A W + I+A++L T + R T +P W Sbjct: 6 NWGIFWEMSPDGIPYIDTLLAGLKWTLATAACAWIMALILGTIFGTLR--TTTKP----W 59 Query: 201 VG------LALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVL-IPE--LLALTLALT 251 V + LF IP L + ++ MPEL F+G W+ +P+ + TLAL Sbjct: 60 VVRIANGYVELFRNIPLLVQMFLW---YFVMPELLPA-FIGDWIKSLPDASFVTATLALG 115 Query: 252 VYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQYLNL 311 +T++ +A V +GI+++ GQ A +LGL T R V++P A R+IIP LT+++ + Sbjct: 116 FFTSSRVAVQVTTGIQALPRGQRMAGAALGLTPVQTYRYVLLPMAFRIIIPALTNEFAAI 175 Query: 312 AKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISLLM 363 KNSS+A IG E+ + ++ T Q E + +Y+ IS+ I+L M Sbjct: 176 IKNSSVALTIGLVELTAA-TYSMREFTFQTFEALTGATIIYVIISV-IALFM 225 Score = 55.8 bits (133), Expect = 1e-12 Identities = 46/156 (29%), Positives = 69/156 (44%), Gaps = 10/156 (6%) Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 Y L GL TL I+A ILG I G R + + ++A YVE+FRNIP L+Q Sbjct: 20 YIDTLLAGLKWTLATAACAWIMALILGTIFGTLRTTTKPWVVRIANGYVELFRNIPLLVQ 79 Query: 122 ILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWP---FVISVVLAIVAI 178 + WYF + P F + S + A +A GF+ + V I A+ Sbjct: 80 MFLWYFVM------PELLPAFIGDWIKSLPDASFVTATLALGFFTSSRVAVQVTTGIQAL 133 Query: 179 VLMTRWANKRFEATGEPFHKF-WVGLALFLVIPALS 213 R A T +++ + +A ++IPAL+ Sbjct: 134 PRGQRMAGAALGLTPVQTYRYVLLPMAFRIIIPALT 169 Lambda K H 0.328 0.141 0.430 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: 239 Number of extensions: 20 Number of successful extensions: 2 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: 375 Length of database: 249 Length adjustment: 27 Effective length of query: 348 Effective length of database: 222 Effective search space: 77256 Effective search space used: 77256 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: 48 (23.1 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