Align citrate lyase β subunit (EC 4.1.3.34) (characterized)
to candidate GFF3000 PGA1_c30490 putative citrate lyase subunit beta
Query= metacyc::MONOMER-16999 (289 letters) >FitnessBrowser__Phaeo:GFF3000 Length = 320 Score = 156 bits (395), Expect = 5e-43 Identities = 103/303 (33%), Positives = 159/303 (52%), Gaps = 22/303 (7%) Query: 2 KPRRSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVYQALQHPLYQDI 61 +P R LF PG+N + AD + DLED+V+ +KD AR V +AL + + Sbjct: 12 RPNRCQLFGPGSNTKLFPKMAASAADVINLDLEDSVAPLDKDVARANVIEALNTVDWGNK 71 Query: 62 ETVVRINPLNTPFGLADL-EAVVRAG--VDMVRLPKTDSKEDIHELEAHVERIERECGRE 118 VRIN L+TP+ D+ + + +AG +D + +PK ED++ ++A V IER GR Sbjct: 72 YISVRINGLDTPYWYRDVVDLLEQAGDRLDQIMIPKVGCAEDVYAVDALVTAIERAKGR- 130 Query: 119 VGSTKLMAAIESALGVVNAVEIARASPRLAAIALAAFDYVMDMG---TSRGDGTELFY-- 173 IESA G+ + IA ASPRL A++L A D+ MG T G E +Y Sbjct: 131 AKPISFEVIIESAAGIAHVEAIAAASPRLQAMSLGAADFAASMGMQTTGIGGTQEDYYML 190 Query: 174 -------------ARCAVLHAARVAGIAAYDVVWSDINNEEGFLAEANLAKNLGFNGKSL 220 A+ A++ A R GI D + D ++++G++A+A + LG GK Sbjct: 191 RAGEKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDDGYIAQAKRSATLGMVGKWA 250 Query: 221 VNPRQIELLHQVYAPTRKEVDHALEVIAAAEEAETRGLGVVSLNGKMIDGPIIDHARKVV 280 ++P+QI L +QV+ P+ + V A E++AA E+A+ G G G+++D I A +V Sbjct: 251 IHPKQIALANQVFTPSDEAVGEAREILAAMEQAKANGEGATVYKGRLVDIASIKQAEVIV 310 Query: 281 ALS 283 A S Sbjct: 311 AQS 313 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: 172 Number of extensions: 10 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: 320 Length adjustment: 27 Effective length of query: 262 Effective length of database: 293 Effective search space: 76766 Effective search space used: 76766 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: 48 (23.1 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