Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 8501055 DvMF_1791 2-isopropylmalate synthase (RefSeq)
Query= BRENDA::D0VY45 (540 letters) >FitnessBrowser__Miya:8501055 Length = 514 Score = 435 bits (1119), Expect = e-126 Identities = 234/514 (45%), Positives = 325/514 (63%), Gaps = 17/514 (3%) Query: 25 VRILDTTLRDGEQSPGAAMTCVQKLETARQLAKLGVDIIEAGFPCASKQDFMAVKMIAEE 84 +RI DTTLRDGEQSPGA M +K+ ARQL LGVDI+EAGFP +S+ DF AV+ IA Sbjct: 8 IRIFDTTLRDGEQSPGATMNLQEKIRLARQLETLGVDIMEAGFPASSQGDFEAVQAIARA 67 Query: 85 VGNCVDGNGYVPVITGVSRCNEKDIATAWEALKHAKRPRLRTFIATSPIHMEYKLRKSKD 144 V + G+ R DI AWEA+K A+ PR+ TF+ATSP+HM+YKLRK D Sbjct: 68 VKGVE--------VAGLCRAMPADIDRAWEAVKVAENPRIHTFLATSPVHMQYKLRKEPD 119 Query: 145 QVLETARNMVKFARSLGCTDIQFGAEDAARSDKEFLYQIFGEVIKAGATTLTIPDTVGIA 204 QV+E A V+ A ++++F AEDA+RS+ +FL ++F VI AGATT+ +PDTVG A Sbjct: 120 QVVEMAVAAVRHAAKY-TSNVEFSAEDASRSNPDFLVRVFEAVINAGATTINVPDTVGYA 178 Query: 205 MPFEYGKLIADIKANTPGIENAIMATHCHNDLGLATANTIEGARYGARQLEVTINGIGER 264 P E+G+LI + NTP A+ + HCHNDLG+ ANT+ + GARQ EVTI+GIGER Sbjct: 179 QPEEFGRLIRYVIENTPNSHKAVFSVHCHNDLGMGVANTLAALKAGARQAEVTISGIGER 238 Query: 265 AGNASFEEVVMALTCRGIDILGGLHTGINTRHILKTSKMVEKYSGLHLQPHKALVGANAF 324 AGNAS EE+VMAL R L G+ T + T +++ G + P+KA+VGANAF Sbjct: 239 AGNASLEEIVMALHTR--RDFYQLDCGVVTEQLFPTCRLLSMIIGQPIPPNKAIVGANAF 296 Query: 325 LHESGIHQDGMLKHRGTYEIISPEDIGLVRSVGDTIVLGKLSGRQALRNRLEELGYKLKD 384 HESGIHQDGMLK+R TYEI++PE IG ++ +V+GK SGR A++N+L+ELGY+L++ Sbjct: 297 AHESGIHQDGMLKNRETYEIMTPESIGKTKT---DLVIGKHSGRNAVKNKLDELGYRLEE 353 Query: 385 TEVEGVFWQFKAVAEKKKRITDTDLRALVSNEAFNEQPIWKLGDLQVTCGTVGFSTATVK 444 ++ VF K +A+KKK+I D D+ ALV E + +++L +L V C G Sbjct: 354 AQLVTVFEAVKKLADKKKQIYDEDIEALVLEEVYRLPDLYRLVNLSVQCSDTGMPPTAAV 413 Query: 445 LFSIDGSMHVACSIGTGPVDSAYKAINHIVKEPAKLVKYTLGAITEGIDATATTSVEISR 504 + + G + A G GP+D+ + I IV L +Y++ AIT G DA +V + + Sbjct: 414 VMDVMGEVKRAAGFGVGPIDAVFNVIGEIVGRAPVLERYSVTAITGGTDAQGEVTVRLRQ 473 Query: 505 GDTNHPVFSGTGGGTDVVVSSVDAYLSALNNMLR 538 N G G D++++S AY++ALN + + Sbjct: 474 ---NGSSAVGRGSDPDIILASARAYVNALNRLAK 504 Lambda K H 0.318 0.134 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: 622 Number of extensions: 31 Number of successful extensions: 6 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: 540 Length of database: 514 Length adjustment: 35 Effective length of query: 505 Effective length of database: 479 Effective search space: 241895 Effective search space used: 241895 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