Align D-galactosamine-6-phosphate deaminase AgaS; GalN-6-P deaminase; Glucosamine-6-phosphate deaminase; GlcN-6-P deaminase; EC 3.5.99.-; EC 3.5.99.6 (characterized)
to candidate 17209 b3136 tagatose-6-phosphate ketose/aldose isomerase (NCBI)
Query= SwissProt::A0KYQ7 (386 letters) >FitnessBrowser__Keio:17209 Length = 384 Score = 298 bits (762), Expect = 2e-85 Identities = 168/372 (45%), Positives = 230/372 (61%), Gaps = 21/372 (5%) Query: 30 WTAKEISQQPKMW-RKVSEQHSDNRTIAAWLTPILAKPQLRIILTGAGTSAYIGDVLAAH 88 WT +EI QP+ W R ++ + + +L P+L K LRIILTGAGTSA+IGD++A Sbjct: 15 WTEEEIRHQPRAWIRSLTNIDALRSALNNFLEPLLRKENLRIILTGAGTSAFIGDIIAPW 74 Query: 89 IQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAAVELAEQLVD 148 + H + A+ TTD+V++P YL P LLIS+GRSGNSPES+AAVELA Q V Sbjct: 75 LASH---TGKNFSAVPTTDLVTNPMDYLNPAHPLLLISFGRSGNSPESVAAVELANQFVP 131 Query: 149 DCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLATLLIFAP-- 206 +CYHL ITCN G L + + + +P ETHD FAMTSS T M + L +FAP Sbjct: 132 ECYHLPITCNEAGALYQNAINSDNAFALLMPAETHDRGFAMTSSITTMMASCLAVFAPET 191 Query: 207 -NSQALMQCIEMAEHILTERLADIR--LQSEQPSKRVVFLGGGPLKAIAQEAALKYLELT 263 NSQ + + ILT L D + P KR+V+LG G L+ A+E+ALK LELT Sbjct: 192 INSQTFRDVADRCQAILTS-LGDFSEGVFGYAPWKRIVYLGSGGLQGAARESALKVLELT 250 Query: 264 AGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELKRDNQALSVLT 323 AG++ + ++SP GFRHGPKSLVD T V+V +SS PYTRQYD DL+ EL+RDNQA+ V+ Sbjct: 251 AGKLAAFYDSPTGFRHGPKSLVDDETLVVVFVSSHPYTRQYDLDLLAELRRDNQAMRVIA 310 Query: 324 LSEE-----------LLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSPDNPCPTGQV 372 ++ E +L S +V F+++ Q A+ +++ + +PD P +G V Sbjct: 311 IAAESSDIVAAGPHIILPPSRHFIDVEQAFCFLMYAQTFALMQSLHMGNTPDTPSASGTV 370 Query: 373 NRVVQGVNVYPF 384 NRVVQGV ++P+ Sbjct: 371 NRVVQGVIIHPW 382 Lambda K H 0.319 0.133 0.392 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: 348 Number of extensions: 13 Number of successful extensions: 4 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: 386 Length of database: 384 Length adjustment: 30 Effective length of query: 356 Effective length of database: 354 Effective search space: 126024 Effective search space used: 126024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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