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 6937022 Sama_1196 phosphosugar isomerase (RefSeq)
Query= SwissProt::A0KYQ7 (386 letters) >FitnessBrowser__SB2B:6937022 Length = 397 Score = 385 bits (990), Expect = e-112 Identities = 194/361 (53%), Positives = 260/361 (72%), Gaps = 4/361 (1%) Query: 27 GAFWTAKEISQQPKMWRKVSEQHSDNRT-IAAWLTPILAKPQLRIILTGAGTSAYIGDVL 85 G+ WTA+EI QQP++WR+++EQ ++ + + P+LA P LR+ILTGAGTSAYIG+ L Sbjct: 26 GSQWTAEEICQQPRLWREMAEQFVQEKSRLQDFAAPLLALPDLRVILTGAGTSAYIGEAL 85 Query: 86 AAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAAVELAEQ 145 A + +PL Q VEAI+TTD+VSHP LYL PTL+IS+GRSG+SPESMAA+EL + Sbjct: 86 APFLATQMPLVGQTVEAIATTDLVSHPHLYLHPARPTLVISFGRSGSSPESMAAIELCDA 145 Query: 146 LVDDCYHLAITCNGQGKLANYCADKSH-CYLYKLPDETHDVSFAMTSSFTCMYLATLLIF 204 L+ CYHL +TCN QG +A Y ++ L+ +P+ +HD SFAMTSSF+CMYL LL+F Sbjct: 146 LLPRCYHLLLTCNPQGSMARYGEQQAQRACLWLMPEGSHDRSFAMTSSFSCMYLGVLLLF 205 Query: 205 APNSQALMQCIEMAEHILTERLADIRLQSEQPSKRVVFLGGGPLKAIAQEAALKYLELTA 264 A N AL + + +AE +L +R+ +I + P RVVFLGGG L+ IA+EAALK LEL+A Sbjct: 206 AANYSALARAVTLAERMLCDRVDEIAKLAALPLSRVVFLGGGTLQGIAREAALKLLELSA 265 Query: 265 GQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELKRDNQALSVLTL 324 G V+ ESPLGFRHGPKSL+D + V+V+ SS+PY R YD D+ EL+RD A +++ L Sbjct: 266 GAVMGVHESPLGFRHGPKSLIDKDSLVVVLCSSEPYARAYDMDMAAELERDGAASALVRL 325 Query: 325 SEELLTGSSG--LNEVWLGLPFILWCQILAIYKAIQLKVSPDNPCPTGQVNRVVQGVNVY 382 EE + + L +VWL P+IL+CQ+ A +KA+ L +S DNPCP GQVNRVVQGV +Y Sbjct: 326 CEENVGADAQTLLEDVWLTFPYILYCQLFAYFKALNLGISADNPCPGGQVNRVVQGVKIY 385 Query: 383 P 383 P Sbjct: 386 P 386 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: 383 Number of extensions: 15 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: 397 Length adjustment: 31 Effective length of query: 355 Effective length of database: 366 Effective search space: 129930 Effective search space used: 129930 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