Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF1451 HP15_1416 L-carnitine dehydratase/bile acid-inducible protein F
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Marino:GFF1451 Length = 401 Score = 228 bits (581), Expect = 2e-64 Identities = 136/406 (33%), Positives = 212/406 (52%), Gaps = 18/406 (4%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 G L +R++DL+ +++GP A ILAD GA+VIK+E P GD TR+ A Sbjct: 3 GPLDGIRIIDLTAMISGPLATMILADQGAEVIKIENPAGGDFTRS--------AANRQGD 54 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 +A YL+ NRNK+SV ++ + G+ + L A +D+ ++NF+ G + GL + L+ + Sbjct: 55 MSALYLNNNRNKKSVALNLKKKAGRDALLRLVASADVFVQNFRPGVIERMGLGEEQLRKV 114 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 P L+ SI+GFG TGPY++R YD +IQGL GL ++ G + P V L D L Sbjct: 115 APNLVMVSISGFGDTGPYSQRPVYDPLIQGLSGLATVQA---GADELRPQLVRTILPDKL 171 Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLT--TGNAPKRLGNAH 239 TG+ + AI AAL R+ G QH+ +++LD +A L + M T P++ + Sbjct: 172 TGVTAAQAITAALFARERTGESQHVRLSMLDAIIAFLWSSDMGSQTFVHSEVPQQEAASL 231 Query: 240 PNIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299 +++ + T G + V +D +++ +P+WA+DPRF T ++R N + L Sbjct: 232 QDLI----YETTTGYITIAVQSDREWQALIRAVDRPEWAEDPRFLTARLRQENIDARLEL 287 Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVA 359 I+ T W+ +LE VPC P+ QV PQV A L H AG++ Q Sbjct: 288 IQSVIKTDTAEHWLARLEAEQVPCAPVLTRTQVLDHPQVLANDLLSHYDHPQAGRLRQAR 347 Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGV 405 +P R S P ++ P LGE T E+L G + A ++G+ Sbjct: 348 APSRFSAAPEQHWQGAPRLGEQTGELLAE-CGYSAEEIQAMCDSGI 392 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: 435 Number of extensions: 29 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: 406 Length of database: 401 Length adjustment: 31 Effective length of query: 375 Effective length of database: 370 Effective search space: 138750 Effective search space used: 138750 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: 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