Align galactaro-1,5-lactonase (characterized)
to candidate Ac3H11_3954 hypothetical protein, not 6-phosphogluconolactonase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3954 Length = 343 Score = 240 bits (613), Expect = 3e-68 Identities = 138/339 (40%), Positives = 203/339 (59%), Gaps = 9/339 (2%) Query: 18 TIAYVSHADSQDIYVLRLNNDGSVNLIDKV-DTGSTVMPLAISPDRKYLYASLRREPYAV 76 T+ +VS ADS +++VL L+++ + ++V G +MP+A+SPD K LY + R +P AV Sbjct: 5 TLVFVSCADSGELHVLHLSSETGLLRTEQVLALGGQLMPMALSPDGKRLYVARRSDPLAV 64 Query: 77 ASYAIDPASGKLKALSKAPLADNMANIATDRSGRYLLAASYFGNKISVNAIGSDGAVQTP 136 + A+D +G+ + L +A L +MA++ATD +GR+LL+ASY + ++V AI +DG V Sbjct: 65 VTLAVDARAGRAEVLGEAALPASMAHVATDGTGRWLLSASYGADLVAVQAIAADGVVAAG 124 Query: 137 PLAVI-PTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGAVTPNTPPSVASKAGA 195 A TG++AHS P N FV A++LG + +YRFD A+GA+ P P A AG Sbjct: 125 RGATTYATGRHAHSALASPGNRFVLAASLGGGQLHRYRFDAATGALQPTDPAVFALPAGT 184 Query: 196 GPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSALPEGFQSSEQLAAADL 255 GPRH F+ +Y ELDA V +D +G L LL S LP G S+ ADL Sbjct: 185 GPRHLRFNARGDRIYLLGELDACVHVLGWDEASGGLELLQSLPTLPPG--STGPAWGADL 242 Query: 256 HLTPDGRFLYATERTSNTLTGYRVDRASGKLTRILNIPTETQPRAFNIDPQGRYLLAVGQ 315 HL+ DG +LY +ER S+TL G+ VD +G+L I T+ QPR F I P GR+L+A GQ Sbjct: 243 HLSADGHWLYTSERNSHTLAGFAVDAVTGRLAPIDYWSTQLQPRGFVITPDGRHLIAAGQ 302 Query: 316 ---KAGLTSYAIDAASGTLTPLFRYTLGRNPNWVEIIDL 351 + G+ + I SG LT + + +G NPNW+ ++ + Sbjct: 303 ISHRVGV--HLIAPGSGALTQVAEHDVGLNPNWITVLPM 339 Lambda K H 0.316 0.131 0.375 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: 397 Number of extensions: 32 Number of successful extensions: 9 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: 352 Length of database: 343 Length adjustment: 29 Effective length of query: 323 Effective length of database: 314 Effective search space: 101422 Effective search space used: 101422 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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