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_008812474.1 M988_RS15870 SIS domain-containing protein
Query= SwissProt::A0KYQ7 (386 letters) >NCBI__GCF_001655005.1:WP_008812474.1 Length = 397 Score = 300 bits (767), Expect = 6e-86 Identities = 162/372 (43%), Positives = 241/372 (64%), Gaps = 13/372 (3%) Query: 23 LTQYGAFWTAKEISQQPKMWRKVSEQHSDNRTI-AAWLTPILAKPQLRIILTGAGTSAYI 81 L + A TA+EI QQP++W+++ ++ + + +L P+LA P L+I+L GAG+SA+ Sbjct: 12 LQDHHALHTAREIDQQPRLWQQLHDELTQAKAYWQPFLQPLLANPDLQIVLCGAGSSAFA 71 Query: 82 GDVLAAHIQQHLPLATQQVEAISTTDIVSHPELYLRGNIPTLLISYGRSGNSPESMAAVE 141 G +A +++ L V A +TDIV P YL PTLL+SYGRSGNSPES+AAV Sbjct: 72 GRAVAPWLREQCGL---DVVAYGSTDIVPSPLQYLDPERPTLLVSYGRSGNSPESVAAVR 128 Query: 142 LAEQLVDDCYHLAITCNGQGKLANYCADKSHCYLYKLPDETHDVSFAMTSSFTCMYLATL 201 LA+Q++ C+HL +TCN G LA Y +S+ +P +HD SFAMTSSF+CM LAT+ Sbjct: 129 LADQILPHCHHLMLTCNPDGALARYAEGRSNVCSLIMPQGSHDQSFAMTSSFSCMTLATI 188 Query: 202 LIFAPNS--QALMQCIEMAEHILTER---LADIRLQSEQPSKRVVFLGGGPLKAIAQEAA 256 L+ P + Q+ +MA ++E+ +++ + KRV+ LG IA+EAA Sbjct: 189 LLLGPLTLEQSAPSLQQMAALCISEQQHWQQQVKVLAGSGFKRVMVLGSRCFTGIAEEAA 248 Query: 257 LKYLELTAGQVVSAFESPLGFRHGPKSLVDSHTQVLVMMSSDPYTRQYDNDLIQELKRDN 316 LK LELTAG++ + ++S +G RHGPK +VD T VL+MMSS+ Y +YD DL++EL+ DN Sbjct: 249 LKMLELTAGRIATRYDSSMGVRHGPKFMVDGDTLVLLMMSSEVYCHRYDADLLRELRHDN 308 Query: 317 QALSVLTLSE----ELLTGSSGLNEVWLGLPFILWCQILAIYKAIQLKVSPDNPCPTGQV 372 A ++ LS +S L+++WL P++++ Q+LA ++ L ++PDNPCPTG+V Sbjct: 309 LAKKIVALSGTPGISDTVFNSDLDDIWLLFPYLMYLQMLAFETSLALGMTPDNPCPTGEV 368 Query: 373 NRVVQGVNVYPF 384 NRVV+GV +YPF Sbjct: 369 NRVVKGVEIYPF 380 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: 407 Number of extensions: 14 Number of successful extensions: 5 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 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