Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_090274851.1 BLU11_RS15305 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_900105005.1:WP_090274851.1 Length = 746 Score = 111 bits (277), Expect = 8e-29 Identities = 108/406 (26%), Positives = 166/406 (40%), Gaps = 48/406 (11%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L L+VLDL LAGP+A +LADLGA+VIKVE P GD R F RG Sbjct: 384 LHGLKVLDLGAYLAGPFACMMLADLGAEVIKVEAPA-GDAMRRLERIFSGTQRG------ 436 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 K V + Q V L +D++ N ++ +DYD LK INP Sbjct: 437 ---------KLGVALKLGDELSQPAVEALVRWADVVHHNMRLPAARKLQVDYDCLKLINP 487 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 QL+YC ++ +G TGP A G+D ++Q G +G G P+ + + D G Sbjct: 488 QLLYCHVSAYGPTGPRADWPGFDQLMQASCGWEV----EQGGAGQPPMWLRFGVGDFFAG 543 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 L S +L L R G GQ ++ +LL + ++ + L + Sbjct: 544 LSSLYVLLLGLYQRARTGEGQMVNASLLGATLLTMSEAVAREDGSVTPIAHLDATQTGLC 603 Query: 244 -PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302 ++ + +DG + + ++F +AG A +V A Sbjct: 604 DTHRLYCCSDGWVAVAALAPEEAQRFHALAG----------ADPEVHFA----------- 642 Query: 303 ATVFKTTAEWVTQLEQAGVPCGPIND--LAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360 +T E + L VP + + L +P A GL H G++ Q+ + Sbjct: 643 ---AQTQTEALLSLSAHDVPAEAVLEAQLDPFLDNPDHAAAGLHTRYQHAEYGELQQIGA 699 Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 + P+ PP LG+H+ EVL LG+ + + AGV+ Sbjct: 700 FWDFGDLPLSLDRPPPALGQHSREVLGG-LGIGDIELDRLAAAGVV 744 Score = 79.7 bits (195), Expect = 3e-19 Identities = 93/387 (24%), Positives = 141/387 (36%), Gaps = 55/387 (14%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L LRV+ L +A AG L + GA+VI VE PGN AR + Sbjct: 6 LHGLRVVSLGSGIASAAAGLHLCEAGAEVILVEPPGN-------------PARRQE---- 48 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 A + NR K+SVT+D P+GQ+ + +L A +D+ I F A L L P Sbjct: 49 ALFAVLNRGKRSVTLDIDVPDGQQQLEQLLAAADVFIHEFTSKQAATLTLGDAQLAERFP 108 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 LI +ITG+ + P A+ + ++ GL+ + GPV V + + L Sbjct: 109 GLIVSAITGWPKKHPLAEAMPRETLVLARLGLLD----EQPGHREGPVFVRMPFANWLAS 164 Query: 184 LYSTAAILAALAHRDH--VGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241 ++A L RD GG H +A A L M++ Sbjct: 165 WLCVVGVMARLIARDRDGQGGSAHTSLA-----QAALVPMTMHWSRAEKPTPAFAKGLDK 219 Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQ----------PQWADD---PRFATNKV 288 +P ADG +I + + A+ + QW P F N+ Sbjct: 220 HIPIPLHQCADGRWIHVHYSPDKSPWMADAMAELGEAEVARLNAQWPPSHVAPNFGANRA 279 Query: 289 RVANRAVLIPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELP 348 +A R + EWV Q V ++ D Q + G +E+ Sbjct: 280 IIATR--------------SAQEWVEHFWQHDVSAQIAAPFGDIYFDEQARLNGYVVEVE 325 Query: 349 HLLAGKVPQVASPIRLSETPVEYRNAP 375 GK Q +++ R+AP Sbjct: 326 DATLGKTLQPGPAWKITPPARIGRSAP 352 Lambda K H 0.319 0.137 0.408 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: 727 Number of extensions: 42 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 406 Length of database: 746 Length adjustment: 36 Effective length of query: 370 Effective length of database: 710 Effective search space: 262700 Effective search space used: 262700 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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