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 WP_008991496.1 I215_RS08190 SIS domain-containing protein
Query= SwissProt::A0KYQ7 (386 letters) >NCBI__GCF_000300875.1:WP_008991496.1 Length = 380 Score = 273 bits (698), Expect = 6e-78 Identities = 160/379 (42%), Positives = 235/379 (62%), Gaps = 23/379 (6%) Query: 21 EQLTQYGAFWTAKEISQQPKMWRKV-SEQHSDNRTIAAWLTPILAKPQLRIILTGAGTSA 79 + +T Y T KEI QP++W + S + IA +L+PIL LRIILTGAG+SA Sbjct: 3 KDITTYINKHTEKEIKAQPRLWNETFSLLVETKKDIALFLSPILQLKDLRIILTGAGSSA 62 Query: 80 YIGDVLAAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAA 139 ++G+V IQQ L TQ V +TTD+V+HPE + PTLLIS+ RSGNSPES+ A Sbjct: 63 FVGEVAQGTIQQQTNLPTQLV---ATTDLVTHPEAFFIKQRPTLLISFARSGNSPESLEA 119 Query: 140 VELAEQLVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLA 199 L +Q D+ YHL ITCN +GKLAN+ K+ Y +LP+ET+D S AMTSSFT M L Sbjct: 120 ASLLDQHCDNAYHLIITCNPEGKLANFDT-KNPLYSIQLPEETNDKSLAMTSSFTAMLLT 178 Query: 200 TLLIF-----APNSQALMQCIEMAEHILTERLADIRLQSEQPS-KRVVFLGGGPLKAIAQ 253 LL+F QA+ I + E +L + D+ + + + +RVVFLG GP+ IA+ Sbjct: 179 ALLVFDIDNIESKQQAVTNMIAIGEDLL--KAEDVFKEIAKSNFERVVFLGSGPMVGIAR 236 Query: 254 EAALKYLELTAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELK 313 E LK ELT GQV+ +S LGFRHGP+++V+++T V+ + S+DP+ +Y+ DL +++ Sbjct: 237 ECHLKLQELTDGQVICKHDSFLGFRHGPRAVVNANTLVVYLFSNDPHVFRYEKDLAEDIA 296 Query: 314 RDNQALSVLTLSEE----------LLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSP 363 RD + + LT+++E ++T + ++ +P L Q+L ++K++ L + P Sbjct: 297 RDARKIQSLTITDEPTLELENSKHIVTSAFKHSDNLNAVPTTLVGQLLGLHKSLTLGLDP 356 Query: 364 DNPCPTGQVNRVVQGVNVY 382 DNP +G +NRVVQGV +Y Sbjct: 357 DNPSVSGAINRVVQGVTIY 375 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: 336 Number of extensions: 16 Number of successful extensions: 6 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: 380 Length adjustment: 30 Effective length of query: 356 Effective length of database: 350 Effective search space: 124600 Effective search space used: 124600 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 24 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