Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate Synpcc7942_2111 Synpcc7942_2111 xylose repressor
Query= reanno::Pedo557:CA265_RS11300 (313 letters) >FitnessBrowser__SynE:Synpcc7942_2111 Length = 302 Score = 148 bits (374), Expect = 1e-40 Identities = 93/306 (30%), Positives = 156/306 (50%), Gaps = 12/306 (3%) Query: 7 IGIDVGGSSLKCGVVNQNGEILYSIIVSLKNAKTQGAIIALIVEAIHTCAKKFKNPILGV 66 IG+D+GG+++K G G+ + V T + A +VEAI + + L + Sbjct: 8 IGVDLGGTAMKLGRYTIEGQCQQELTVPTPTPSTPSNVRAALVEAIRQLDPQAE--ALAI 65 Query: 67 GIGFPGII-YNNKIIAGADNLPGFKQLALGEILQEVTRYNIVMDNDANLMGLGEMTYGAA 125 GIG PG ++ A NL G+ ++ L + L+ + +++ NDAN GLGE+ G Sbjct: 66 GIGTPGPADAAGRVARVAINLDGWTEVPLADWLEADLQRPVILANDANCAGLGEVWLGGG 125 Query: 126 KDCSDVVFLTVGTGIGGAVMIDNKLYGGFRNRGTELGHIVVQHNGLACACGGRGCLEAYA 185 + D + LT+GTG+GGA++++ +L+ G ELG I + G C G +G LE YA Sbjct: 126 RGYRDAILLTLGTGVGGAIVLNGELFVGRTGTAAELGLITLDPAGPHCNSGNQGSLEQYA 185 Query: 186 SVTALLNHYQSIHPNPPEEIDGKYMVEKYLAREEYAVEAMESHFDYLATGIISFVNVFSP 245 S+ A+ + D K + ++ + A+ A + + LA G+ S V V +P Sbjct: 186 SIGAVQRRF---------GCDPKDLGDRASQGDPEAIAAWQDYGRTLAAGLASLVYVLTP 236 Query: 246 QKIVIGGGISESGAFYVREIERRIKTLAVPIAPGNELVVAARLGNKAGLLGCAANVFQKF 305 + I++GGGIS S AF++ + + +P + + + A LGN+AG +G A + K Sbjct: 237 EVIILGGGISGSAAFFLPALTEELHRRVLPTSREDLQIAIAALGNEAGRVGAAKLAWDKL 296 Query: 306 KAFDYV 311 +A V Sbjct: 297 QALGKV 302 Lambda K H 0.321 0.140 0.408 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: 237 Number of extensions: 12 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: 313 Length of database: 302 Length adjustment: 27 Effective length of query: 286 Effective length of database: 275 Effective search space: 78650 Effective search space used: 78650 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: 48 (23.1 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