Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_011840177.1 RSPH17029_RS00595 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000015985.1:WP_011840177.1 Length = 381 Score = 411 bits (1057), Expect = e-119 Identities = 214/383 (55%), Positives = 261/383 (68%), Gaps = 13/383 (3%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L+ +RV++L+R+LAGPWAGQ+LADLGADV+KVE P GDDTR WGPPF++ E A Sbjct: 5 LAGIRVVELARILAGPWAGQVLADLGADVVKVEAP-EGDDTRRWGPPFIER---EGDRSA 60 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 AY+ +ANR K+SVT DF PEGQ VR L A +D++IENFKVGGLA YGLD+ SL+ +NP Sbjct: 61 AYFHAANRGKRSVTADFRTPEGQETVRRLVADADVVIENFKVGGLAKYGLDWPSLQKVNP 120 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183 +L+YCSITGFGQ GPYA RAGYDF+IQG+ GLMS+TG EG P KVGVA+TDI TG Sbjct: 121 RLVYCSITGFGQDGPYAHRAGYDFIIQGMAGLMSVTGAAEGQ----PQKVGVAVTDIFTG 176 Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243 +Y+ AILAAL R G GQ +DMAL+DV +ANQAMNYL TG AP+++GN HPN+ Sbjct: 177 IYAATAILAALHQRAGTGRGQQVDMALMDVAAGIMANQAMNYLATGVAPRKMGNEHPNLA 236 Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303 PY F ADG I+ GND Q+R+ + G P A P F TN RVANRA L + Sbjct: 237 PYAVFDCADGWIIIATGNDAQYRRLCTLLGLPGLATAPAFLTNADRVANRAELTRALTAV 296 Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363 T AE + E GVP GPIND+A+VFADPQ++ RG+ + VP V SP R Sbjct: 297 TSGWRKAELLAACEAEGVPAGPINDMAEVFADPQIRHRGM-----QIAPDGVPGVRSPFR 351 Query: 364 LSETPVEYRNAPPLLGEHTLEVL 386 SE + P LGEH EVL Sbjct: 352 FSEAKLALARPAPRLGEHQAEVL 374 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: 512 Number of extensions: 29 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: 381 Length adjustment: 31 Effective length of query: 375 Effective length of database: 350 Effective search space: 131250 Effective search space used: 131250 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 Apr 10 2024. 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