Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_059151198.1 V474_RS09170 SIS domain-containing protein
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_001046635.1:WP_059151198.1 Length = 358 Score = 302 bits (773), Expect = 1e-86 Identities = 181/342 (52%), Positives = 217/342 (63%), Gaps = 6/342 (1%) Query: 12 TLMEREAAEAGAAVSRMLAANRDAIERVAARLRASPPAVVVTCARGSSDHAATYAKYLIE 71 T M REA EA A ++ L N D + +LR P T ARGSSD AA +AK+L+E Sbjct: 17 TQMAREAREAPALCAQQLRLNADLVRDAGRQLRDLAPPFAATLARGSSDQAAAFAKFLLE 76 Query: 72 TLTGVPTASAALSVASLYDAPVAPGNGLCL-AISQSGKSPDLLATVEHQRKAGAFVVAMV 130 T VPT S A SV SLY A A + L AISQSG+SPDLLA + R+ GA V+A+V Sbjct: 77 THARVPTLSHAPSVGSLYHATSANFRNVPLIAISQSGRSPDLLAAAKDAREQGAIVIAVV 136 Query: 131 NAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWAQDEALETAVADLPA 190 N SPLA LA IVIP+ AGPE SVAATKS++C L A+ L A W+QDEAL A+ Sbjct: 137 NDAASPLAQLAQIVIPVHAGPETSVAATKSFVCMLVALTHLAAEWSQDEALLAALESTGE 196 Query: 191 QLERAFALDWSAAVTALTGASGLFVLGRGYGYGIAQEAALKFKETCALHAESFSAAEVRH 250 LE A DW+ AVT L AS + VLGRG IA EAALK KET +LHAE+FS AEV H Sbjct: 197 VLETAAIADWTDAVTLLQDASEMLVLGRGPTLPIAGEAALKLKETSSLHAEAFSIAEVAH 256 Query: 251 GPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLA----DPAARQAGLPA-IA 305 GPM +VGE VLA A D A +R+ +A+F +RGA V+ A D A LP+ Sbjct: 257 GPMTLVGEGSAVLALAPLDVARTGLRDRLADFAARGAHVIAAGAPEDVAPAGLVLPSRTD 316 Query: 306 AHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNKVTETL 347 HP + I +QSFY +ANAL+LARG +PDSPPHLNKVT TL Sbjct: 317 VHPVLGAIAQIQSFYGLANALSLARGRNPDSPPHLNKVTRTL 358 Lambda K H 0.317 0.128 0.360 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: 367 Number of extensions: 14 Number of successful extensions: 3 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: 347 Length of database: 358 Length adjustment: 29 Effective length of query: 318 Effective length of database: 329 Effective search space: 104622 Effective search space used: 104622 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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