Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate WP_011841833.1 RSPH17029_RS13630 malonyl-CoA synthase
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_000015985.1:WP_011841833.1 Length = 501 Score = 163 bits (413), Expect = 1e-44 Identities = 149/512 (29%), Positives = 226/512 (44%), Gaps = 43/512 (8%) Query: 67 KAGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPE 126 K G RLS AF+ LL+R + E L+ GDR+ V + K PE Sbjct: 24 KDGTRLSGDAFF----------------RLLARTAHALRAEG--LRPGDRIAVQVAKSPE 65 Query: 127 WWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLH 186 A + G V +P T T ++ Y L + + + D APA+ VA + H Sbjct: 66 ALAVYGAAVALGAVFLPLNTAYTPAEVDYFLGDATPRIFLCDSAQAPALTPVAER----H 121 Query: 187 SKLIVSQHSREGWGNLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSF 246 +++ + +G G+L + M+ + ++ A+ +TSGTTG K + + Sbjct: 122 GARLLTLDA-DGTGDLAQRMRDRPEEIGAEPRGAQDLAALLYTSGTTGRSKGAMLSQRNL 180 Query: 247 GLGLSVNGRFWLDLIASDVMWNTSDTGWAKSAW-SSVFSPWTQGACVFAHYLPRFESTSI 305 W DV+ + + +S + T GA VF LP F+ +I Sbjct: 181 LSNAEALADLWR-FTERDVLIHALPIFHTHGLFVASNVTLLTGGAMVF---LPGFDLEAI 236 Query: 306 LQTLSKFPITVFCSAPTAY-RMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGL 364 L+ + + T PT Y R+L ++ ++ VS P+ + ++ +TG Sbjct: 237 LRWMPE--ATALMGVPTFYTRLLSDPRLTRALAAGMRLFVSGSAPLLADTHAEFEARTGH 294 Query: 365 DIYEGYGQTETVLICGNFKGMKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVL 424 I E YG TET + N + + G++G P P +++IL + G + PG+ G V+ Sbjct: 295 RILERYGMTETNMSTSNPYEGERRAGTVGFPLPGVELRILAQ-GREVAPGEIG-----VI 348 Query: 425 PERPFGLFTHYVDNPSKTASTLR-GSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIG 483 R +F Y P KTA LR F++TGD G D +GY V R D+I+S GY I Sbjct: 349 EVRGPNVFQGYWQMPEKTAEELRPDGFFVTGDLGCRDAEGYVQIVGRQKDLIISGGYNIY 408 Query: 484 PFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKT 543 P EVE L E P + ESAVV P P GE A +V P Q L + Sbjct: 409 PKEVELLLDEQPGVLESAVVGLPHPDLGEAALAVLVPRPGVTLDPQAVLGA-----IADR 463 Query: 544 TAPYKYPRKVEFIEELPKTVSGKVKRNELRKK 575 A +K PR +EELP+ GKV++ LR + Sbjct: 464 LARFKQPRAAVLVEELPRNTMGKVQKTLLRAR 495 Lambda K H 0.319 0.134 0.416 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: 587 Number of extensions: 30 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 580 Length of database: 501 Length adjustment: 35 Effective length of query: 545 Effective length of database: 466 Effective search space: 253970 Effective search space used: 253970 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: 52 (24.6 bits)
This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 2024.
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