Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate GFF3085 PGA1_c31360 putative hydroxypyruvate reductase
Query= BRENDA::O58231 (440 letters) >FitnessBrowser__Phaeo:GFF3085 Length = 424 Score = 229 bits (583), Expect = 2e-64 Identities = 153/437 (35%), Positives = 236/437 (54%), Gaps = 20/437 (4%) Query: 5 DIREIGLRLVGEAIKAADPYRAVLNAVKVSDDKIIVQGKEFEIKGKVYVIALGKAACEMA 64 D+R I R A+ A+P A+ +++ + G G++ ++ALGKAA M Sbjct: 3 DLRSIARRFFAAAVARANPATALAESLRQHPPTLPQPG------GRLILVALGKAAIPMI 56 Query: 65 RAIEDILDVED-GVAVTKYGYGKELKRIKVIEAGHPIPDEKSILGAKEALSILNRAREND 123 R +L D +AVT +L ++V+ HP+P S+ S L+ D Sbjct: 57 RQAMAMLPPPDRAIAVTNPENVADLSDVEVLAGNHPVPHHMSLAAGDALRSALSNLNAKD 116 Query: 124 IVFILISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKGGKLAK 183 V LISGGGSAL P G++L D TDLLL G I ++N +R+ +S++KGG L + Sbjct: 117 RVIALISGGGSALAVAPAGGLTLADKTAVTDLLLGGGVDITQMNLIRQQLSELKGGGLLR 176 Query: 184 MIKGTGIV-LIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESVRLHIE 242 + + I+SDV+GD+L AIASGPTV + A+ L +++WE +P +V+ H+ Sbjct: 177 AAQPAQVFSYILSDVIGDDLRAIASGPTVAPLGSRAMARDCLLSHNLWEGLPHAVQTHLT 236 Query: 243 RGLRGEVEETLKEDLPNVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLEGEAKDAGL 302 + + + + H LI SN S A+ +A R G+ A+I++ L G+ + A Sbjct: 237 TPEEPQ-QSPANSSVTSAH--LIGSNRHSLGAVRDQATRDGWSAHIVSDALIGDVEVAAT 293 Query: 303 FIGSIVQEIAERGRPFEPPVVLVFGGETTVTIEGKGGKGGPNQEIALSAT---RKISDLE 359 I + +E E GR P L+FGGETTV + G G+GG NQE+AL R+ Sbjct: 294 EILAATKE-QETGR----PTALIFGGETTVQLTG-SGRGGRNQELALHIARLGRRALKER 347 Query: 360 ALIVAFDTDGTDGPTDAAGGIVDGTTYKKLREKGIDVEKVLKEHNSYEALKKVGGLLFTG 419 ++ TDG DGPTDAAGG+VD T++++ + G + + +L+ ++S ALK G LL TG Sbjct: 348 WTFLSAGTDGRDGPTDAAGGVVDSGTWQRIGDNGGNPDALLRNNDSNAALKLAGDLLITG 407 Query: 420 PTGTNVNSIVIAIVTSK 436 TGTNV + I +++ + Sbjct: 408 GTGTNVADVQIMLLSPR 424 Lambda K H 0.315 0.137 0.376 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: 427 Number of extensions: 17 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: 440 Length of database: 424 Length adjustment: 32 Effective length of query: 408 Effective length of database: 392 Effective search space: 159936 Effective search space used: 159936 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: 42 (22.0 bits) S2: 51 (24.3 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