Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate SMa1406 SMa1406 TtuD3 hydroxypyruvate reductase
Query= reanno::psRCH2:GFF1145 (423 letters) >FitnessBrowser__Smeli:SMa1406 Length = 419 Score = 379 bits (973), Expect = e-110 Identities = 207/419 (49%), Positives = 268/419 (63%), Gaps = 2/419 (0%) Query: 1 MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG 60 M+ + + L +LF++A+ AA P+ L LP+ GR +V+GAGK AA +A A E +W G Sbjct: 1 MSPEDRDFLSELFEAAVGAADPKLALRARLPQRPRGRTVVVGAGKGAAQLAAAFESLWGG 60 Query: 61 ELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGG 120 L G+VVTRY + C RI V+EAAHPVPD G + + E V L D V+ L GG Sbjct: 61 PLEGVVVTRYGYAVHCDRIRVIEAAHPVPDCNGLIASHALFEAVRGLTPDDLVVALFCGG 120 Query: 121 GSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYT 180 GS+LL P E ++L D+ A+N+ALL SGA I MN +RK +S IKGGRLA AC PA V + Sbjct: 121 GSALLPCPPEELALEDEIALNRALLASGAPISVMNAIRKQVSRIKGGRLAAACHPAKVIS 180 Query: 181 YAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGD 240 + +SDVPGD+ +ASGPTV D T A + + + IE+P + WL+ P D Sbjct: 181 FIVSDVPGDDPAQVASGPTVPDATDRAAARAMRDAWRIELPERLVDWLKGENGTAPSPND 240 Query: 241 PMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLH 299 P+ + ++IA+ + SL+AAA A A GI +IL D +EGEAR+V KVHA IAR+VVL Sbjct: 241 PVFAGHEVQVIASARLSLEAAAARADALGIPAIILSDAIEGEARDVGKVHAAIAREVVLR 300 Query: 300 GQPIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSE 359 +P P V+LSGGETTVT+RG+GRGGRN EFLL+L +GL + +LA DTDGIDGSE Sbjct: 301 NRPFERPVVLLSGGETTVTLRGHGRGGRNTEFLLSLAIAAEGL-SFASLAADTDGIDGSE 359 Query: 360 DNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418 NAGA S R LG L+ ND + F L+DL V GPT TNVNDFRAIL+ Sbjct: 360 SNAGAFADGSSATRLRALGRDPVALLSGNDAWTAFNCLEDLFVPGPTGTNVNDFRAILV 418 Lambda K H 0.316 0.134 0.384 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: 449 Number of extensions: 17 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: 423 Length of database: 419 Length adjustment: 32 Effective length of query: 391 Effective length of database: 387 Effective search space: 151317 Effective search space used: 151317 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 (21.6 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