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_057508604.1 ABB28_RS10505 SIS domain-containing protein
Query= SwissProt::A0KYQ7 (386 letters) >NCBI__GCF_001431535.1:WP_057508604.1 Length = 386 Score = 291 bits (745), Expect = 2e-83 Identities = 170/370 (45%), Positives = 231/370 (62%), Gaps = 19/370 (5%) Query: 27 GAFWTAKEISQQPKMWRKVSEQHSD-NRTIAAWLTPILAKPQLRIILTGAGTSAYIGDVL 85 GA WTA+EI+QQP M + + + A++ P++ P R+ILTGAGTSAYIG L Sbjct: 18 GALWTAREIAQQPAMLQATHALVASLAEQLRAFVAPLVDDPGARVILTGAGTSAYIGQCL 77 Query: 86 AAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAAVELAEQ 145 A + + L +V+A+ TTDIV P+LYL P LL+S+GRSGNSPES+AAVELAE Sbjct: 78 APLLDRQL---AARVDAVPTTDIVCAPQLYLDPGQPLLLVSFGRSGNSPESLAAVELAEA 134 Query: 146 LVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLATLLIFA 205 LV D HL +TCN G LA ++ L LP++THD SFAMTSSF+CM ATL + Sbjct: 135 LVGDIRHLVVTCNPAGALARIPVAQAMTLL--LPEQTHDTSFAMTSSFSCMMYATLAALS 192 Query: 206 PNSQALMQCIEMA---EHILTERLADIRLQSEQPSKRVVFLGGGPLKAIAQEAALKYLEL 262 P + + +A E ++ L +R + + RVV+LG G L+ +A+EA+LK EL Sbjct: 193 PAAALDARIAPIARATEAVIDGALPLLRTLAAARNDRVVYLGSGLLQGLAREASLKLGEL 252 Query: 263 TAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELKRDNQALSVL 322 T G VV+ F+SPLGFRHGPK+ V T V+V +S+DPYTR+YD+DLI EL+RD A V+ Sbjct: 253 TNGAVVTCFDSPLGFRHGPKTFVTDDTLVIVFVSNDPYTRRYDHDLIDELRRDGCAARVV 312 Query: 323 TLSEE----------LLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSPDNPCPTGQV 372 +S + + G +V L P++ QI A+ +++ V+PDNP P G V Sbjct: 313 EISAQPRAGALDDTLAVPGLERAEDVDLLWPYVAAAQIYALLHSLERGVTPDNPNPAGIV 372 Query: 373 NRVVQGVNVY 382 NRVVQGV +Y Sbjct: 373 NRVVQGVQLY 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: 369 Number of extensions: 19 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: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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