Align (R)-citramalate synthase (EC 2.3.1.182) (characterized)
to candidate Echvi_2061 Echvi_2061 Isopropylmalate/homocitrate/citramalate synthases
Query= reanno::Btheta:351386 (499 letters) >FitnessBrowser__Cola:Echvi_2061 Length = 504 Score = 617 bits (1592), Expect = 0.0 Identities = 299/499 (59%), Positives = 391/499 (78%), Gaps = 2/499 (0%) Query: 1 MDTTLRDGEQTSGVSFVPHEKLMIARLLLEDLKVDRVEVASARVSEGEFEAVKMICDWAA 60 MDTTLRDGEQTSGVSF+P EKL IA+LLLE+L+VDR+EVASARVSEGE E VK I WAA Sbjct: 1 MDTTLRDGEQTSGVSFLPSEKLQIAKLLLEELRVDRIEVASARVSEGELEGVKKITHWAA 60 Query: 61 RRNLLQKVEVLGFVDGHTSVDWIQRTGCRVINLLCKGSLKHCTQQLKKTPEEHIADIINV 120 + L VEVLGFVD SVDW+ G +V+NLL KGSL H T QLKKTP EH A I Sbjct: 61 EKGYLDCVEVLGFVDTPASVDWLTEAGAKVLNLLTKGSLNHLTHQLKKTPVEHFAAIEKC 120 Query: 121 VHYADEQDIGVNVYLEDWSNGMKDSPEYVFQLMDGLKQTSIRRYMLPDTLGILNPLQVIE 180 +HYA+E+ I VNVYLEDWS+GM+ S +Y +L+ L +++R MLPDTLG+L P +V E Sbjct: 121 IHYANEKGISVNVYLEDWSSGMRHSRDYTLELIAFLADQNVKRVMLPDTLGLLKPAEVAE 180 Query: 181 YMRKMKKRYPNTHFDFHAHNDYDLAVSNVLAAVLSGVRGLHTTINGLGERAGNAPLSSVQ 240 Y+ + +++P HFDFHAHNDYDL+V+NV+ A+ G+ G+HTT+NGLGERAGNAPL SV Sbjct: 181 YVGLVSEQFPEVHFDFHAHNDYDLSVANVMEAINHGISGIHTTVNGLGERAGNAPLESVV 240 Query: 241 AILKDHFNAMTNIDESRLNDVSRVVESYSGIVIPANKPIVGENVFTQVAGVHADGDNKNN 300 A L D N+ E+++ +S++VE +SG+ IP+NKP+VGENVFTQ AG+HADGDNK N Sbjct: 241 ATLSDFTTVKLNVQENKIYRISKLVEQFSGLHIPSNKPVVGENVFTQTAGIHADGDNKKN 300 Query: 301 LYCNDLLPERFGRKREYALGKTSGKANIRKNLEDLGLELDEDAMRKVTERIIELGDKKEL 360 LY NDLLPERFGR R+YALGKTSGKANI KNL +LG++L+ + + KVT++IIELGD+KE Sbjct: 301 LYFNDLLPERFGRTRKYALGKTSGKANILKNLLELGIKLEPEELSKVTQKIIELGDRKER 360 Query: 361 VTQEDLPYIVSDVLKHGAIGEKVKLKSYFVNLAHGLKPMATLKIEINGKEYEESSSGDGQ 420 VT EDLPYI+SDVL++ +I + + ++ Y + + GLKP LK++ + YE +SG+GQ Sbjct: 361 VTTEDLPYIISDVLQNNSIKKDISIEGYHMTHSKGLKPTVQLKLKFKDQFYEAHASGNGQ 420 Query: 421 YDAFVRALRKIYKVTLGRKFPMLTNYAVSIPPGGRTDAFVQTVITWNYDEQVFRTRGLDA 480 +D+F+ AL+KIYK +L +K P LT+++VSIPPGG+TDAFV+TVITW+Y ++ +T+GLD+ Sbjct: 421 FDSFMLALQKIYK-SLNKKLPKLTDFSVSIPPGGKTDAFVETVITWDYG-RIIKTKGLDS 478 Query: 481 DQTEAAIKATMKMLNLLEE 499 DQT AA+ AT KMLN++E+ Sbjct: 479 DQTVAAMMATEKMLNIIEQ 497 Lambda K H 0.318 0.135 0.390 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: 730 Number of extensions: 27 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: 499 Length of database: 504 Length adjustment: 34 Effective length of query: 465 Effective length of database: 470 Effective search space: 218550 Effective search space used: 218550 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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