Align Homocitrate synthase 1; EC 2.3.3.14 (uncharacterized)
to candidate 408370 DVUA0016 homocitrate synthase
Query= curated2:Q44290 (377 letters) >MicrobesOnline__882:408370 Length = 384 Score = 201 bits (512), Expect = 2e-56 Identities = 132/363 (36%), Positives = 190/363 (52%), Gaps = 6/363 (1%) Query: 4 VLINDTTLRDGEQAAGVVFTLEEKVAIAKFLDTIGVPELEVGIPAMGEEEMRAICAI-SN 62 V++ D+TLR+G QA GV F ++ +I + + GV E E G G++++ A + + Sbjct: 22 VMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEAEAGWA--GQDDLAATLRLGAR 79 Query: 63 LGLKANLLAWNRAVISDIKASVACGMERVHIAIPVSGIQIAAKFHGQWRVSLQRLKDCIS 122 + L W R +D+ + G RVHI +P S + + LQR+ + Sbjct: 80 VAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAHMRLRLGMGRDEVLQRVTTVLE 139 Query: 123 FAVDQG-LWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYGKVKL 181 A G L V +G ED+ RA + L +A A GA R R DTVG+L P V L Sbjct: 140 HAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHRLRCSDTVGLLTPDGMVRLVLL 199 Query: 182 LVSALTIPVEVHTHNDFGMATANALAGIKAGASSVNTTVIGLGERAGNAALEEVVMAIKR 241 A +PV VH HND G+ATANALA + AGA + +++GLGERAG EE+ A+ Sbjct: 200 ARRASALPVAVHCHNDLGLATANALAALDAGADGADVSLLGLGERAGITRAEELAAALVV 259 Query: 242 IYGVDMGIDTPRLLELSQLVAAASGANVPPWKAIVGENTFAHESGIHAHGVLQNPDTYEP 301 + G +D L + + +AA+ +PP A+ GEN FA ESG+H HGV ++P +EP Sbjct: 260 LRGESYRLD--MLRGVCRRLAASLEMRLPPHWAVAGENLFAVESGVHLHGVQRDPALFEP 317 Query: 302 FAPEEVGWERRLVVGKHSGRHSVSNLLEQHGIFLNPEETQSVLDAVRQQSIKKKRSLTTE 361 F P VG ERRL VG G V+ + HG+ L + + + AVR ++ R LT Sbjct: 318 FPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDALRRHVRAVRDKACSLGRPLTDA 377 Query: 362 ELL 364 E L Sbjct: 378 EFL 380 Lambda K H 0.318 0.133 0.388 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: 382 Number of extensions: 17 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: 377 Length of database: 384 Length adjustment: 30 Effective length of query: 347 Effective length of database: 354 Effective search space: 122838 Effective search space used: 122838 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 Aug 03 2021. The underlying query database was built on Aug 03 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