Align citrate lyase β subunit (EC 4.1.3.34) (characterized)
to candidate Pf1N1B4_5615 Citrate lyase beta chain (EC 4.1.3.6)
Query= metacyc::MONOMER-16999 (289 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5615 Length = 271 Score = 106 bits (264), Expect = 6e-28 Identities = 89/283 (31%), Positives = 139/283 (49%), Gaps = 27/283 (9%) Query: 5 RSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVYQAL-QHPLYQDIET 63 RS LF+P + + GAD V+ DLEDAV K+ AR + + L +HP Q Sbjct: 7 RSALFVPATRPERIPKAIASGADRVIVDLEDAVQENLKEQARDNLERFLSEHPAAQ---V 63 Query: 64 VVRINPLNTPFGLADLEAVVR-AGVDMVRLPKTDSKEDIHELEAHVERIERECGREVGST 122 +VR+N ADL+ R AGV + LPK +S + + + + + S Sbjct: 64 LVRVNAPEHWAHAADLDLCRRHAGVTAILLPKAESAAQVSTAFSTGKPV----WPIIESA 119 Query: 123 KLMAAIESALGVVNAVEIARASPRLAAIALAAFDYVMDMGTSRGDGTE---LFYARCAVL 179 K +AA+ S G A+ + RL+ + D +D+ + G L +AR AVL Sbjct: 120 KGLAALSSIAG-------AKGAERLS---FGSLDLGLDLNLTTGSSAAEEILSHARYAVL 169 Query: 180 HAARVAGIA-AYDVVWSDINNEEGFLAEANLAKNLGFNGKSLVNPRQIELLHQVYAPTRK 238 RVAG+A A D V+ I + G A+++GF G ++P Q+ ++HQ P+ + Sbjct: 170 LCTRVAGLAPALDGVFPSIADTAGLHNAVQFARDMGFGGALCIHPSQVAIIHQALKPSPE 229 Query: 239 EVDHALEVIAAAEEAETRGLGVVSLNGKMIDGPIIDHARKVVA 281 E+ A +I EA + G GV L+G+M+D P+I A ++A Sbjct: 230 ELLWAQRII----EAASAGDGVFVLDGQMVDAPVIGRAHSILA 268 Lambda K H 0.319 0.134 0.375 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: 157 Number of extensions: 12 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: 289 Length of database: 271 Length adjustment: 26 Effective length of query: 263 Effective length of database: 245 Effective search space: 64435 Effective search space used: 64435 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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