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 206897 DVU1453 long-chain-fatty-acid--CoA ligase
Query= SwissProt::Q3UNX5 (580 letters) >MicrobesOnline__882:206897 Length = 564 Score = 205 bits (522), Expect = 3e-57 Identities = 159/529 (30%), Positives = 253/529 (47%), Gaps = 67/529 (12%) Query: 90 SFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLT 149 S+ +L LL+ +FA L A + GDRV V+LP +P+ +A L+ G ++ Sbjct: 47 SYAKLRLLAERFAANL-RAQGVLPGDRVSVMLPNVPQAIIAFWGLLKAGCTVVMTNPLYM 105 Query: 150 QKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQH--------------- 194 +K++++++ S A+ +I A+D V K E L +L + + Sbjct: 106 EKELVHQIHDSGAEYMI-------ALDLVWPKIEPLRDRLGIRKFFITRISDALGFPLNL 158 Query: 195 ------SREG-WGNL----------KEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPK 237 REG W ++ K + K V+ + + + +T GTTG K Sbjct: 159 LYRFKAKREGTWRDVPFDGETVIPWKTLFKKKEGYSAKVENPREALALLQYTGGTTGISK 218 Query: 238 MIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAK-----SAWSSVFSPWTQGACV 292 + TH + LSVN + ++ + G + + P GA + Sbjct: 219 GVMLTHYN----LSVNVQQIKAILGESTRMRHTFLGLMPYFHVYGLTTCLTLPTALGATI 274 Query: 293 FAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQN-DMSSYKFNSLKHCVSAGEPIN 351 PR+ +L + K T+F AP+ Y L+Q D+ + S+K+C+S P+ Sbjct: 275 IP--FPRYVPRDVLVGIDKHKPTIFPGAPSIYISLMQQKDVGEFDLKSIKYCISGSAPMP 332 Query: 352 PEVMEQWRKKTGLDIYEGYGQTET--VLICGNFKGMKIKPGSMGKPSPAFDVKILD-ENG 408 E + ++ + TG + EG+G TE V G++ KPGS+G P P + +++D E G Sbjct: 333 LEHIRRFHELTGAQVIEGFGLTEASPVTHLNPIHGVQ-KPGSIGVPFPDTEARVVDMEVG 391 Query: 409 AT-LPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWF 467 LPPG+ G++ + R + Y++ P +TA+TLR + TGD MDEDGYF+ Sbjct: 392 LVPLPPGKIGELII-----RGPQVMQGYLNRPDETANTLRNGWLYTGDIATMDEDGYFFI 446 Query: 468 VARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSH 527 V R D+I+ GY + P E++ L EHP + E+ V P RGE++KA+IV K Sbjct: 447 VDRKKDMIIVGGYNVYPREIDEVLHEHPKVKEAVTVGVPHATRGEIIKAYIVPREGVK-- 504 Query: 528 DQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKKE 576 K EI H ++ A YK P++VEF ELPKT+ GKV R LR +E Sbjct: 505 ---LTKAEIVAHCREQLANYKVPKQVEFRNELPKTIVGKVLRRILRAEE 550 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: 770 Number of extensions: 38 Number of successful extensions: 7 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: 580 Length of database: 564 Length adjustment: 36 Effective length of query: 544 Effective length of database: 528 Effective search space: 287232 Effective search space used: 287232 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: 53 (25.0 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