Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate SMc02877 SMc02877 hypothetical protein
Query= reanno::Phaeo:GFF2746 (342 letters) >FitnessBrowser__Smeli:SMc02877 Length = 340 Score = 354 bits (908), Expect = e-102 Identities = 185/337 (54%), Positives = 241/337 (71%) Query: 5 TKMRREIDEIPTAVDRLLSHGRVEIEAVADAARALDPNVMVTVARGSSDHVCTYLKYASE 64 T MRREIDEIP A RLL + A RA DP +VT+ARGSSDH +LKYA E Sbjct: 3 TNMRREIDEIPEAAARLLERSATRLAQAGAALRAKDPAFLVTIARGSSDHAALFLKYAIE 62 Query: 65 IMLGVPVASVGPSVASIYKAPLRLKGALSLAVSQSGKSPDIVSMAGSARKDGALSVALTN 124 + G PVAS+GPS+ASIY A L+L GA ++A+SQSGKSPDIV+MA +A + GA+S+ALTN Sbjct: 63 LTTGRPVASLGPSLASIYGADLKLGGAAAIAISQSGKSPDIVAMAEAATRAGAVSIALTN 122 Query: 125 DAASPLAAAADHTLDIHAGPELSVAATKTFVTSAVAGLWLLAQWDRNQAVLAALHALPEQ 184 SP+A A H LDI AGPE++VAATK++V S VAGL +L +W + + A+ LP Q Sbjct: 123 TLPSPIAEACTHPLDILAGPEIAVAATKSYVNSIVAGLAVLGEWTGDATLKHAVADLPNQ 182 Query: 185 LDRACRIDWPEVRDAIGARSSLFTLGRGQALAVSNEAALKFKETCQLHAESYSSAEVLHG 244 L +A ++DW + + SL+ LGRG ALA+++EAALKFKET +HAE+YS+AEVLHG Sbjct: 183 LAKAVKLDWQDFAGDLAEAESLYVLGRGPALAIASEAALKFKETSGMHAEAYSAAEVLHG 242 Query: 245 PVSIVEEGFPVLGFAAADAAEGALAGIADQIAAKGAQVFATTDKVTAARRVDHVRTDHAL 304 PV++V FPVL AA DAAE ++A IAD ++AKGA V T+ + A+R+ V T H L Sbjct: 243 PVALVGHRFPVLVLAARDAAEASVADIADGMSAKGAVVHVTSARAGKAKRLPFVETGHPL 302 Query: 305 TDPISLIVSFYAMVEAFAASRGIDPDAPRHLKKVTET 341 TD ++LI+ FY VEA++ SRG++PDAP +LKKVTET Sbjct: 303 TDALALILPFYGFVEAWSRSRGLNPDAPENLKKVTET 339 Lambda K H 0.317 0.129 0.364 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: 292 Number of extensions: 9 Number of successful extensions: 1 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: 342 Length of database: 340 Length adjustment: 29 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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 (21.7 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