Align Citrate lyase alpha chain; Citrase alpha chain; Citrate (pro-3S)-lyase alpha chain; Citrate CoA-transferase subunit; EC 4.1.3.6; EC 2.8.3.10 (characterized)
to candidate 3608020 Dshi_1427 Citrate CoA-transferase (RefSeq)
Query= SwissProt::P75726 (510 letters) >FitnessBrowser__Dino:3608020 Length = 515 Score = 302 bits (774), Expect = 2e-86 Identities = 179/469 (38%), Positives = 252/469 (53%), Gaps = 1/469 (0%) Query: 37 QAEKARDRKLCANLEEAIRRSGLQDGMTVSFHHAFRGGDLTVNMVMDVIAKMGFKNLTLA 96 +A+ RKL LE G+ DG T+SFHH +R GD V VM + + G K LT+ Sbjct: 48 RADAGDGRKLRPGLEVVFDELGIADGRTLSFHHHYRDGDRVVVEVMRLARERGLKGLTIC 107 Query: 97 SSSLSDCHAPLVEHIRQGVVTRIYTSGLRGPLAEEISRGLLAEPVQIHSHGGRVHLVQSG 156 SS+ H+ LV + G +T I T +RGP+A+ I+ V + SHGGR + SG Sbjct: 108 PSSIFPTHSSLVPLLEDGTITSIVTDYMRGPVADWITAHPGRVTVLLQSHGGRARAISSG 167 Query: 157 ELNIDVAFLGVPSCDEFGNANGYTGKACCGSLGYAIVDADNAKQVVMLTEELLPYPHNPA 216 +L IDVAF+G D GN G G CG LGY VDA AK V + ++ Sbjct: 168 QLKIDVAFVGASLADRRGNLTGRAGALACGPLGYPAVDAQYAKATVGMAHDVTDAALPRV 227 Query: 217 SIEQDQVDLIVKVDRVGDAAKIGAGATRMTTNPRELLIARSAADVIVNSGYFKEGFSMQT 276 I VDL+V +R GDA +I +G+T + P IA ++D+I +G E F++Q+ Sbjct: 228 DIPARFVDLVVPFERPGDANRIRSGSTVPSETPLSRGIAERSSDIIAAAGLLTEEFALQS 287 Query: 277 GTGGASLAVTRFLEDKMRSRDIRADFALGGITATMVDLHEKGLIRKLLDVQSFDSHAAQS 336 G GG SLA + + ++ +R F GGIT+ V+L G+ R + DVQ FD A +S Sbjct: 288 GAGGYSLAAVPHVGSLLAAQGMRGAFMSGGITSAHVELLRAGVFRAIRDVQCFDLEAVRS 347 Query: 337 LARNPNHIEISANQYANWGSKGASVDRLDVVVLSALEIDTQFNVNVLTGSDGVLRGASGG 396 NP+H ++A +YA+ VD L V++L A+E+D FNVNV++G+DG + G GG Sbjct: 348 AIENPDHQMMTAAEYASPLHPNPCVDDLSVMLLGAVEVDFGFNVNVVSGTDGRILGGPGG 407 Query: 397 HCDTAIASALSIIVAPLVRGRIPTLVDNVLTCITPGSSVDILVTDHGIAVNPARPELAER 456 H D A + LSI++ L G +V V TPG VD++VT+ G A+NPAR +L R Sbjct: 408 HPDAARGADLSIVLTSLTGGGFAKIVPAVRCVSTPGVDVDVVVTEAGFAINPARADLVAR 467 Query: 457 LQEAGIKVVSIEWLRERARLLTGEPQPIEFTDRVVAVVRYRDGSVIDVV 505 L AG+K V IE L A P +R + RDG ++D V Sbjct: 468 LTRAGLKPVEIEDLARIAGAQAAH-SPAPLAERPSVHIERRDGLILDWV 515 Lambda K H 0.319 0.134 0.384 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: 714 Number of extensions: 41 Number of successful extensions: 1 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: 510 Length of database: 515 Length adjustment: 35 Effective length of query: 475 Effective length of database: 480 Effective search space: 228000 Effective search space used: 228000 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 (21.7 bits) S2: 52 (24.6 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