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 BWI76_RS04450 BWI76_RS04450 citrate lyase subunit alpha
Query= SwissProt::P75726 (510 letters) >FitnessBrowser__Koxy:BWI76_RS04450 Length = 508 Score = 697 bits (1800), Expect = 0.0 Identities = 355/479 (74%), Positives = 413/479 (86%), Gaps = 1/479 (0%) Query: 31 SPKQTYQAEKARDRKLCANLEEAIRRSGLQDGMTVSFHHAFRGGDLTVNMVMDVIAKMGF 90 SP ++EK R RK+CA+LEEAIRRSGLQ+GMT+SFHHAFRGGD VNMV+ +A+MGF Sbjct: 28 SPWLASESEK-RQRKICASLEEAIRRSGLQNGMTISFHHAFRGGDKVVNMVVAKLAEMGF 86 Query: 91 KNLTLASSSLSDCHAPLVEHIRQGVVTRIYTSGLRGPLAEEISRGLLAEPVQIHSHGGRV 150 ++LTLASSSL D H PL+EHI+ GV+ +IYTSGLRG L EEIS GL+ PVQIHSHGGR Sbjct: 87 RDLTLASSSLIDAHWPLIEHIKNGVIRQIYTSGLRGKLGEEISAGLMENPVQIHSHGGRA 146 Query: 151 HLVQSGELNIDVAFLGVPSCDEFGNANGYTGKACCGSLGYAIVDADNAKQVVMLTEELLP 210 +LVQSGELNIDVAFLGVP CDE+GNANG++GK+ CGSLGYA VDAD AK VV+LTEE + Sbjct: 147 YLVQSGELNIDVAFLGVPCCDEYGNANGFSGKSRCGSLGYAKVDADAAKCVVLLTEEWVD 206 Query: 211 YPHNPASIEQDQVDLIVKVDRVGDAAKIGAGATRMTTNPRELLIARSAADVIVNSGYFKE 270 YP+ PASI QDQVDLIV+VD VGD AKI AGA R+T+NPRELLIAR AA VI +SGYFK+ Sbjct: 207 YPNYPASIAQDQVDLIVQVDEVGDPAKITAGAIRLTSNPRELLIARQAAKVIEHSGYFKD 266 Query: 271 GFSMQTGTGGASLAVTRFLEDKMRSRDIRADFALGGITATMVDLHEKGLIRKLLDVQSFD 330 GFS+QTGTGGASLAVTRFLEDKMR +I A F LGGIT TMVDLHEKGLI+ LLD QSFD Sbjct: 267 GFSLQTGTGGASLAVTRFLEDKMRRHNITASFGLGGITGTMVDLHEKGLIKALLDTQSFD 326 Query: 331 SHAAQSLARNPNHIEISANQYANWGSKGASVDRLDVVVLSALEIDTQFNVNVLTGSDGVL 390 AA+SLA NPNHIEISANQYAN GSKG + +RL+VV+LSALEIDT FNVNV+TGS+GVL Sbjct: 327 GDAARSLANNPNHIEISANQYANPGSKGIACERLNVVMLSALEIDTGFNVNVMTGSNGVL 386 Query: 391 RGASGGHCDTAIASALSIIVAPLVRGRIPTLVDNVLTCITPGSSVDILVTDHGIAVNPAR 450 RGASGGHCDTA + L+II APLVRGRIP +V+ VLT +TPG+SVD+LVTDHGIAVNPAR Sbjct: 387 RGASGGHCDTAAGADLTIITAPLVRGRIPCVVEKVLTRVTPGASVDVLVTDHGIAVNPAR 446 Query: 451 PELAERLQEAGIKVVSIEWLRERARLLTGEPQPIEFTDRVVAVVRYRDGSVIDVVHQVK 509 +L +RL++A I +++IE L++RA LLTG+P+PI FTDRVVAVVRYRDGSVIDV+HQVK Sbjct: 447 QDLIDRLRQADIPLMTIEALQQRAELLTGKPEPIAFTDRVVAVVRYRDGSVIDVIHQVK 505 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: 826 Number of extensions: 25 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: 508 Length adjustment: 34 Effective length of query: 476 Effective length of database: 474 Effective search space: 225624 Effective search space used: 225624 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