Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ac3H11_3532 L-carnitine dehydratase/bile acid-inducible protein F
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3532 Length = 424 Score = 517 bits (1332), Expect = e-151 Identities = 256/417 (61%), Positives = 317/417 (76%), Gaps = 13/417 (3%) Query: 2 GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61 GAL+ ++VLDLSRVLAGPW Q+LADLGADV+KVERPG GDDTR WGPPFLKDA G +T Sbjct: 9 GALAGIKVLDLSRVLAGPWCTQVLADLGADVVKVERPGVGDDTRQWGPPFLKDAEGNDTN 68 Query: 62 EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121 +A+YY + NRNK+SVTID P+GQ L+R++A ++DI++ENFKVGGL YGLD++SL+A+ Sbjct: 69 QASYYTACNRNKRSVTIDMASPDGQALIRQMAQEADIVVENFKVGGLKQYGLDHESLRAL 128 Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181 NP+LIYCS+TGFGQ GPYA+RAGYD M+Q + GLMS+TG+ + + G GP++VGVA+ D+ Sbjct: 129 NPRLIYCSVTGFGQDGPYAERAGYDLMVQAMTGLMSITGQADTEPGGGPMRVGVAVIDLF 188 Query: 182 TGLYSTAAILAALAHRDH----VGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGN 237 TGLY++ AILAAL RD+ G GQHIDMALLDV +A LANQA +L TG AP R+GN Sbjct: 189 TGLYASNAILAALHVRDNAATGTGQGQHIDMALLDVGMAVLANQASGFLATGKAPGRMGN 248 Query: 238 AHPNIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLI 297 +HP++ PYQDFPT DG+ +L +GNDGQF++F A QPQWA DPRFATN +RV NR LI Sbjct: 249 SHPSLAPYQDFPTQDGNMLLAIGNDGQFQRFCAAANQPQWASDPRFATNTLRVQNRTDLI 308 Query: 298 PLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAG---- 353 P + T +TTA+W+ LE VPCGPIN +AQ F D QVQARGLA+ LP G Sbjct: 309 PAMEAVTRTRTTADWIALLEDKAVPCGPINTIAQAFDDAQVQARGLAVTLPRWKDGEAAT 368 Query: 354 -KVPQ---VASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 KV Q VASP+RLS TP RNAPP LG+HT EVL +GLD A + A R GV+ Sbjct: 369 DKVQQITGVASPLRLSATPPVLRNAPPALGQHTDEVLAE-MGLDAARIAALRAQGVV 424 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: 581 Number of extensions: 26 Number of successful extensions: 3 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: 424 Length adjustment: 31 Effective length of query: 375 Effective length of database: 393 Effective search space: 147375 Effective search space used: 147375 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