Align Putative homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate 207383 DVU1914 2-isopropylmalate synthase/homocitrate synthase family protein
Query= curated2:Q8TW28 (397 letters) >MicrobesOnline__882:207383 Length = 538 Score = 169 bits (429), Expect = 1e-46 Identities = 124/397 (31%), Positives = 197/397 (49%), Gaps = 23/397 (5%) Query: 18 EVIVYDTTLRDGEQTPGVSFTPEQKLEIAHLLDELGVQQIEAGFPVVSEGERDAVRRIAH 77 ++ +YDTTLRDG Q+ ++ KL+IA LDELG+ IE G+P + + + I + Sbjct: 4 QIHLYDTTLRDGSQSEDINLNTPDKLKIALRLDELGIAYIEGGWPGSNPVDVAFFKEIRN 63 Query: 78 EGLN-ADILCLARTLRGDVDAALDCDV--------DGVITFIATSELHLKHKLRMSREEV 128 L A I T A D ++ D F + E H + LR+ Sbjct: 64 YNLKQAKISAFGSTHHPSHTAENDPNLKAIAAARTDAAAIFGKSCERHAREALRLDGRRN 123 Query: 129 LERIADTVEYAKDHGLWVAFSAE---DGTRTEFEFLERVYRTAEECGADRVHATDTVGVM 185 L+ I D++ + K V F AE DG R + V R A E G D + DT G Sbjct: 124 LDIIHDSIAFLKKQVAEVFFDAEHFFDGYRHNAAYALEVLRRAHEAGGDVLVLCDTNGGT 183 Query: 186 IPAAMRLFVAKIREVV-DLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGN 244 +P + V +RE + + +G+H H+D +AVANS+AAV+AGA + T+NG+GER GN Sbjct: 184 LPHEVHDIVTAVREQLPEAKLGIHAHNDCEVAVANSIAAVQAGAVQVQGTMNGVGERCGN 243 Query: 245 AALEEVIMALK----ELYGIDPGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFRHES 300 A L VI L+ Y P + L +S VSE + + + VG +AF H+ Sbjct: 244 ANLSSVIPILELKSAGAYACLPEGRLQQLTAVSSYVSEVTNLPPFSRQPFVGRSAFAHKG 303 Query: 301 GIHVAAVLEEPRTYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELG--VEPEEEIVEEV 358 G+HV+AV YE I P+ VG ++++++ + GR +V+ G ++ +E +V+ + Sbjct: 304 GVHVSAVNRNATLYEHITPESVGNHQRVLITELAGRSNIVSLARRFGFHLDKDEPVVKGL 363 Query: 359 LKRIK---ALGDRRVRVTDSKLEEIVRNVLESRGDRD 392 + +K +LG ++ +E ++ L RG R+ Sbjct: 364 MNELKKKASLG-YDYAAAEASVELLLLRKLARRGVRE 399 Lambda K H 0.317 0.135 0.380 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: 455 Number of extensions: 19 Number of successful extensions: 5 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: 397 Length of database: 538 Length adjustment: 33 Effective length of query: 364 Effective length of database: 505 Effective search space: 183820 Effective search space used: 183820 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 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