Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate WP_084545358.1 H566_RS0117640 glycerate kinase
Query= reanno::psRCH2:GFF1145 (423 letters) >NCBI__GCF_000482785.1:WP_084545358.1 Length = 438 Score = 481 bits (1237), Expect = e-140 Identities = 247/418 (59%), Positives = 311/418 (74%), Gaps = 1/418 (0%) Query: 3 LDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGEL 62 L P LLR + D+AI AA P + +LP+ GR IVIGAGKA+AAMA+A+E W GEL Sbjct: 21 LKPADLLRAMLDAAIRAAQPSRCVPPYLPQLPKGRLIVIGAGKASAAMAKAVEHHWPGEL 80 Query: 63 SGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGS 122 GLV+TR+ + C RI++VEA+HPVPD AG+ ARR+ +LVS L E D V+ L+SGGGS Sbjct: 81 EGLVITRHGYGQPCDRIDIVEASHPVPDAAGQDAARRLHKLVSGLTEDDVVLSLISGGGS 140 Query: 123 SLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYA 182 +LLA P +GI+L DKQ + +ALL SGA I E+NCVR+HLSA+KGGRLA AC PA V Sbjct: 141 ALLAAPIDGITLEDKQDVTRALLASGASISEINCVRRHLSALKGGRLALACAPARVINLL 200 Query: 183 ISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPM 242 ISDVPGD+ IASGP V DPTT A+ I +RY + +P NV LE R E++KPGDP Sbjct: 201 ISDVPGDDPIDIASGPLVPDPTTCADAIAICKRYGLRLPLNVWKVLESGRGESVKPGDPR 260 Query: 243 LSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHGQ 301 L + +IA PQ SL+AAA+VARAAG+TPLILGD +EGEAREV KV AGIA QV+ HG+ Sbjct: 261 LPQIETHIIAAPQASLEAAADVARAAGVTPLILGDSIEGEAREVGKVMAGIALQVLRHGE 320 Query: 302 PIAAPCVILSGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDN 361 P+ PCV+LSGGETTVTVRG+G GGRN EFLL+L L G+ V+A+A DTDG+DG+ + Sbjct: 321 PMNKPCVLLSGGETTVTVRGDGSGGRNVEFLLSLGIALNGVQGVHAIAADTDGVDGAAEI 380 Query: 362 AGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILIL 419 AGA++ P + A+A LG+ AL NNDG+G+F A++D +VTGPT TNVNDFRAIL++ Sbjct: 381 AGAILRPGTLAKARALGISPQQALGNNDGHGFFGAVEDSVVTGPTLTNVNDFRAILVI 438 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: 508 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: 423 Length of database: 438 Length adjustment: 32 Effective length of query: 391 Effective length of database: 406 Effective search space: 158746 Effective search space used: 158746 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: 51 (24.3 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