Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate AZOBR_RS25925 AZOBR_RS25925 type II citrate synthase
Query= BRENDA::Q8NSL1 (383 letters) >FitnessBrowser__azobra:AZOBR_RS25925 Length = 427 Score = 187 bits (476), Expect = 4e-52 Identities = 129/379 (34%), Positives = 187/379 (49%), Gaps = 20/379 (5%) Query: 21 TAVSKVMPETNSLTYRGYAVEDLVENCSFEEVFYLLWHGELPTAQQLAEFNERGRSYRSL 80 +A++ + + L +RGYA++DL ENC + EV +LL GELP QQ EF ER +Y ++ Sbjct: 52 SAITYIDGDEGILLHRGYAIQDLAENCDYLEVCHLLLRGELPNPQQKEEF-ERTITYHTM 110 Query: 81 DAGLISLIHS-LPKEAHPMDVMRTAVSYMGTKDSEYFTT----DSEHIRKVGHTLLAQLP 135 +S +S ++AHPM VM G + Y + D H L+A++P Sbjct: 111 VHEQLSRFYSGFRRDAHPMAVM---CGVTGALSAFYHDSTDILDPRQRMIAAHRLIAKMP 167 Query: 136 MVLAMDIRRRKGLDIIAPDSSKSVAENLLSMVFGTGPESPASNPADVRDFEKSLILYAEH 195 + AM + G + P + S AEN L M FGT E+ +P R +K IL+A+H Sbjct: 168 TMAAMAYKYSVGQPFMYPRNDLSYAENFLYMTFGTPCETWKVDPVLARAMDKIFILHADH 227 Query: 196 SFNASTFTARVITSTKSDVYSAITGAIGALKGPLHGGANEFVMHTMLAIDDPNKAAAWIN 255 NAST T R+ S+ ++ ++ I I AL GP HGGANE V+ + I + +I Sbjct: 228 EQNASTSTVRLAGSSHANPFACIASGIAALWGPAHGGANEAVLLMLEEIGSVERIPKFIK 287 Query: 256 NALDNKNV--VMGFGHRVYKRGDSRVPSMEKSFRE----LAARHDGEKWVAMYEN---MR 306 A D + +MGFGHRVYK D R M ++ E L + + +AM + Sbjct: 288 RAKDKNDPFRLMGFGHRVYKNYDPRAKIMRQTCYEVLDVLGIKDEPHLAIAMELEKIALE 347 Query: 307 DAMDARTGIKPNLDFPAGPAYHLLGFPVDFFTPLFVIARVAGWTAHIVEQYEN--NSLIR 364 D + PN+DF +G +GFP FT LF +AR GW + E E+ + R Sbjct: 348 DPYFVEKKLYPNVDFYSGIILKAMGFPTSMFTVLFALARTVGWISQWQEMIEDPQQKIGR 407 Query: 365 PLSEYNGEEQREVAPIEKR 383 P Y G R P+ KR Sbjct: 408 PRQLYTGNPGRAFVPLNKR 426 Lambda K H 0.318 0.133 0.388 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: 394 Number of extensions: 16 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: 383 Length of database: 427 Length adjustment: 31 Effective length of query: 352 Effective length of database: 396 Effective search space: 139392 Effective search space used: 139392 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