Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_011384532.1 AMB_RS10775 CoA transferase
Query= reanno::pseudo5_N2C3_1:AO356_10845 (406 letters) >NCBI__GCF_000009985.1:WP_011384532.1 Length = 402 Score = 235 bits (600), Expect = 2e-66 Identities = 145/405 (35%), Positives = 210/405 (51%), Gaps = 12/405 (2%) Query: 4 LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63 L +RVLD++ +A P+A IL + GA+VIKVE+PG GD R +G +D ++ Sbjct: 8 LDGIRVLDIATFIAAPYAAAILGEFGAEVIKVEQPGGGDTFRRFGSITERDG------DS 61 Query: 64 AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123 +LS RNK SVT+D +PEG+ L +L A++D++ ENF+ G L +GL ++ L+ +NP Sbjct: 62 LMWLSEARNKNSVTLDLRKPEGRELFLKLVARTDVIAENFRPGTLEKWGLGWEELRRVNP 121 Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVG-VALTDILT 182 LI I+G+GQTGPY R G+ + GGL L G P G PV G +L D ++ Sbjct: 122 GLILLRISGYGQTGPYKDRPGFARIAHAFGGLSYLAGMP----GDVPVTPGSTSLADYMS 177 Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242 GLY +L AL HRD G GQ ID+AL + L A + G +R G N Sbjct: 178 GLYGAIGVLLALRHRDATGEGQVIDLALYESVFRALDEIAPAFAMFGKVREREGAGTVNA 237 Query: 243 VPYQDFPTADGDFI-LTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301 P+ F DG ++ L D F + AE +P+ AD ++ + R+A RA + L+ Sbjct: 238 CPHGHFRCGDGKWVALACTTDRMFARLAEAMERPELADGAKWGLLRNRLAERADVDALVG 297 Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361 + + VP P+N +A +F DPQ QARG +E+ + G V Sbjct: 298 HWAATRPRETVMELCLDFEVPAAPLNTIADIFEDPQFQARGNLLEVADAVLGGVVVPGVV 357 Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406 +LS TP + P LGE V +LGL EA + + GV+ Sbjct: 358 PKLSATPGRVDHLGPRLGEDNARVYGGLLGLGEAEIAELKSKGVI 402 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: 456 Number of extensions: 25 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: 402 Length adjustment: 31 Effective length of query: 375 Effective length of database: 371 Effective search space: 139125 Effective search space used: 139125 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