Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate SM_b21182 SM_b21182 hypothetical protein
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >FitnessBrowser__Smeli:SM_b21182 Length = 394 Score = 421 bits (1083), Expect = e-122 Identities = 217/388 (55%), Positives = 266/388 (68%), Gaps = 8/388 (2%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L +RVL+L+R+LAGPW GQ LADLGADVIKVE P GDDTR WGPPF+ E +A Sbjct: 5 LKGIRVLELARILAGPWIGQTLADLGADVIKVESPA-GDDTRTWGPPFVTGEDDERL-DA 62 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AY+ + NR K+SV +DFT EGQ VR LAA+SD+L+ENFKVGGLA YGLDY+SL +NP Sbjct: 63 AYFHACNRGKRSVVLDFTTAEGQEAVRRLAAQSDVLLENFKVGGLAKYGLDYESLSKVNP 122 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +LIYCS+TGFGQ GPYA RAGYD+++QG+ G+M LTG P+ + P K+GVA DI TG Sbjct: 123 RLIYCSVTGFGQDGPYAHRAGYDYIVQGMSGIMDLTGEPDRE----PQKIGVAFADIFTG 178 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 LY A+ AALA R+ G GQ IDMALLD LANQA+N+L +G AP+RLGNAHPNI Sbjct: 179 LYGVIAVQAALAQRERTGEGQQIDMALLDCMTGVLANQALNFLVSGKAPRRLGNAHPNIA 238 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 PYQ FPT+DG I+ VGND QF KF E+ G+P A D R+ TN RV +R L P + Sbjct: 239 PYQVFPTSDGHLIVAVGNDRQFVKFCELLGRPDLAADARYRTNADRVQHRDSLTPELAAE 298 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPH--LLAGKVPQVASP 361 T + +LE +GVP GPIN +A VFADPQ+ R + ++ PH AG P V +P Sbjct: 299 TAKYERDTLLEKLEASGVPGGPINTVADVFADPQIVHRQMRVDTPHTGAAAGTSPGVRTP 358 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRV 389 IR S + P LGEHT EVL + Sbjct: 359 IRFSGATLALDRGVPRLGEHTAEVLAEI 386 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: 496 Number of extensions: 21 Number of successful extensions: 5 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: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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