Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate 6939130 Sama_3228 glycerate kinase (RefSeq)
Query= BRENDA::P23524 (381 letters) >FitnessBrowser__SB2B:6939130 Length = 384 Score = 434 bits (1115), Expect = e-126 Identities = 231/378 (61%), Positives = 277/378 (73%), Gaps = 7/378 (1%) Query: 1 MKIVIAPDSYKESLSASEVAQAIEKGFREIFPDAQYVSVPVADGGEGTVEAMIAATQGAE 60 MKIVIAPDS+KESLSA EVA AIE GF+ + PDA Y+ +P+ADGGEGTV++++ AT G Sbjct: 1 MKIVIAPDSFKESLSAMEVADAIEAGFKRVLPDATYIKLPMADGGEGTVQSLVDATGGTI 60 Query: 61 RHAWVTGPLGEKVNASWGISGDGKT-------AFIEMAAASGLELVPAEKRDPLVTTSRG 113 VT PLG KV A +G+ G K A IEMAAASGL LV E R+PL+T+S G Sbjct: 61 VPVEVTAPLGNKVEAFFGLLGSAKEKGDSCVRAVIEMAAASGLHLVAPELRNPLLTSSFG 120 Query: 114 TGELILQALESGATNIIIGIGGSATNDGGAGMVQALGAKLCDANGNEIGFGGGSLNTLND 173 TGELIL ALE G T++I+GIGGSATNDGGAGM+ ALG KL A+G+ I GGGSL L+ Sbjct: 121 TGELILAALERGVTHLILGIGGSATNDGGAGMITALGGKLLKADGSPIALGGGSLAELSH 180 Query: 174 IDISGLDPRLKDCVIRVACDVTNPLVGDNGASRIFGPQKGASEAMIVELDNNLSHYAEVI 233 ID++GLDPRL I VACDV NPL G GAS +FGPQKGA+ M+ LD NL+ YA I Sbjct: 181 IDLTGLDPRLAGLTIDVACDVNNPLCGPKGASAVFGPQKGATPEMVTLLDANLARYANCI 240 Query: 234 KKALHVDVKDVPGAGAAGGMGAALMAFLGAELKSGIEIVTTALNLEEHIHDCTLVITGEG 293 + L VKD+PGAGAAGGMGAAL+ LGAELK GI+IV AL L + + D LVITGEG Sbjct: 241 ESTLGKPVKDIPGAGAAGGMGAALVGLLGAELKPGIQIVIEALKLADALADADLVITGEG 300 Query: 294 RIDSQSIHGKVPIGVANVAKKYHKPVIGIAGSLTDDVGVVHQHGIDAVFSVLTSIGTLDE 353 IDSQ+IHGK PIGVA+ AK++ KPVIGIAG L+DD GVVH+HG+DAVF+V+ TL E Sbjct: 301 CIDSQTIHGKTPIGVASCAKQFGKPVIGIAGCLSDDCGVVHEHGLDAVFAVVNRAMTLPE 360 Query: 354 AFRGAYDNICRASRNIAA 371 A A NI + +RN+AA Sbjct: 361 ALATAGTNIEQTARNVAA 378 Lambda K H 0.315 0.135 0.385 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: 481 Number of extensions: 18 Number of successful extensions: 2 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: 381 Length of database: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 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: 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