Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 408370 DVUA0016 homocitrate synthase (TIGR)
Query= BRENDA::A0A0S6UXF5 (400 letters) >FitnessBrowser__DvH:408370 Length = 384 Score = 220 bits (560), Expect = 6e-62 Identities = 140/371 (37%), Positives = 204/371 (54%), Gaps = 8/371 (2%) Query: 4 WRTRMAFPGPTTRSDGVQPRSVVLNDTTLRDGEQAPGVAFTTAEKLSIARALASAGVTEI 63 WR R G + G R V+L D+TLR+G QA GV F A++ SI + +A++GVTE Sbjct: 3 WRRRHV--GLASGLQGHLRRCVMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEA 60 Query: 64 EAGTPAMGHDEVSAIRAIVEADLPATAIG-WCRMRTSDVDAAIEAGVSMVNVSIPASDVQ 122 EAG G D+++A + P+ + WCR T+D+D A EAG V++ +P+SD Sbjct: 61 EAGWA--GQDDLAATLRLGARVAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAH 118 Query: 123 IAAKLSGGRPAALEQVRRVVGYARDSG-LDVAVGGEDSSRADVDFLVELIATAKAAGARR 181 + +L GR L++V V+ +A G L V +G ED+ RA D L L TA GA R Sbjct: 119 MRLRLGMGRDEVLQRVTTVLEHAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHR 178 Query: 182 FRIADTLSVLDPDAAFALLTALRATTDLELEFHGHDDLGLATANTLAAIKAGATHASVTV 241 R +DT+ +L PD L+ R + L + H H+DLGLATAN LAA+ AGA A V++ Sbjct: 179 LRCSDTVGLLTPDGMVRLVLLARRASALPVAVHCHNDLGLATANALAALDAGADGADVSL 238 Query: 242 IGLGERAGNAPLEEVAVALKQLYGRETGVVLSELKHVASVVAAAAARAIPLNKAIVGEHV 301 +GLGERAG EE+A AL L G L L+ V +AA+ +P + A+ GE++ Sbjct: 239 LGLGERAGITRAEELAAALVVLRGE--SYRLDMLRGVCRRLAASLEMRLPPHWAVAGENL 296 Query: 302 FTHESGIHVDGLLKDQRTYQALDPHLLGRSNRIVIGKHSGLAAITALLAELQLSASADEA 361 F ESG+H+ G+ +D ++ P L+G R+ +G G A + A+ L+ D Sbjct: 297 FAVESGVHLHGVQRDPALFEPFPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDAL 356 Query: 362 KSVLARVRQHA 372 + + VR A Sbjct: 357 RRHVRAVRDKA 367 Lambda K H 0.317 0.130 0.362 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: 388 Number of extensions: 21 Number of successful extensions: 4 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: 400 Length of database: 384 Length adjustment: 31 Effective length of query: 369 Effective length of database: 353 Effective search space: 130257 Effective search space used: 130257 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: 50 (23.9 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