Align citrate synthase (unknown stereospecificity) (EC 2.3.3.16) (characterized)
to candidate BWI76_RS19140 BWI76_RS19140 citrate (Si)-synthase
Query= BRENDA::P45858 (372 letters) >FitnessBrowser__Koxy:BWI76_RS19140 Length = 428 Score = 161 bits (408), Expect = 3e-44 Identities = 116/376 (30%), Positives = 186/376 (49%), Gaps = 20/376 (5%) Query: 7 YSPGLDGVIAAETHISYLDTQSSQILIRGYDLIELSETKSYLELVHLLLEGRLPEESEME 66 + PG ++ IS++DT+ S +L RGY + +L+ +LE+ +LL G P+E+ + Sbjct: 43 FDPGFANTAGCKSAISWIDTEKSILLHRGYPVDQLARQCDFLEVAWILLRGDAPDEASYQ 102 Query: 67 TLERKINSASSLPADHLRLLELLPEDTHPMDGLRTGLSALAG-YDRQIDDRSPSANKERA 125 + I S + R+ D+HPM + + LA Y +D +P A Sbjct: 103 DFKNTITRHSLVHEQIARMCSSFRRDSHPMALMCALVGTLAAFYHDVLDVENPEHRALAA 162 Query: 126 YQLLGKMPALTAASYRIINKKEPILPLQTLSYSANFLYMMTGKLPSS------LEEQIFD 179 +LL KMP L A SY+ ++ P LSY+ NFL+M+ +P+ + EQ + Sbjct: 163 TRLLSKMPTLAAMSYKFSIEQPAQYPRNDLSYAGNFLHMLFA-IPAEQYQLNPVIEQAMN 221 Query: 180 RSLVLYSEHEMPNSTFAARVIASTHSDLYGALTGAVASLKGNLHGGANEAVMYLLLEAKT 239 + LVL+++H ST R S+ ++L+ + +ASL G HGGANEA M +L E T Sbjct: 222 QILVLHADHGQCASTTTVRAAGSSGANLFACVAAGLASLWGPAHGGANEASMRMLEEINT 281 Query: 240 TSDFEQLLQTKLKRKEKI---MGFGHRVYMKKMDPRALMMKEALQQLCDKAG--DHRLYE 294 L +K KR + +GFG+ Y + +DPRA +++E ++ ++ G D L Sbjct: 282 VDQIPAFL-SKAKRDPQTFRRLGFGNSRY-RHLDPRAAILRETCHRVLEELGMSDMPLQV 339 Query: 295 MCEAGERLMEK----EKGLYPNLDYYAAPVYWMLGIPIPLYTPIFFSARTSGLCAHVIEQ 350 E + E GL P++D+Y A + +G+P ++ I RT G AH E Sbjct: 340 AMALEEVALTDPYFVENGLSPSVDFYTAVILKAMGLPSSMFVVITAVGRTLGWVAHWNEM 399 Query: 351 H-ANNRLFRPRVSYMG 365 H A ++RPR Y G Sbjct: 400 HEAPLTIYRPRQIYTG 415 Lambda K H 0.317 0.134 0.381 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: 320 Number of extensions: 14 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: 372 Length of database: 428 Length adjustment: 31 Effective length of query: 341 Effective length of database: 397 Effective search space: 135377 Effective search space used: 135377 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 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