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 HSERO_RS00095 HSERO_RS00095 AMP-dependent synthetase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__HerbieS:HSERO_RS00095 Length = 539 Score = 233 bits (593), Expect = 2e-65 Identities = 173/543 (31%), Positives = 259/543 (47%), Gaps = 28/543 (5%) Query: 44 FKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELGLLSRKFAN 103 ++ +IP +FN A+ D+W + A D +G +S+++L +LS +FAN Sbjct: 14 YEWQIPTHFNIAQAACDRWADGS------GRTAIICEDADGSVTSYSYDQLKILSDRFAN 67 Query: 104 ILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILYRLQSSKAK 163 L A + RGDR+ + L + E + ++A + G + +P I YRL +S A Sbjct: 68 AL-RAAGVGRGDRIGIYLSQRIETVITHLAAYKLGAITVPLFYLFGPDAIAYRLDNSGAV 126 Query: 164 CIITDD------TLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKYASDSHTCVD 217 ++TD TLA + A+ S L++ Q + + W L T D Sbjct: 127 ALVTDASGMEKATLAGELPALRLVFCVESSDLVLPQ-TTDFWDRLHAAPAELDPVLTLAD 185 Query: 218 TKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIAS--DVMWNTSDTGWA 275 D M IY TSGTTG K H H LG D D W +D W Sbjct: 186 ---DPAMIIY-TSGTTGKAKGALHAHRVL-LGHLPGVEVSHDSFPQEGDRFWTPADWAWI 240 Query: 276 KSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLV-QNDMSS 334 + G V A L +F++ + L++ I PTA +ML + + Sbjct: 241 GGLLDVLLPSLYHGVAVVARRLEKFDAAEVFGLLARHQIRNVFFPPTALKMLRGAATVRA 300 Query: 335 YKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKIK-PGSMG 393 SL+ S GE + +++ R+ G+ I E YGQTE L+ + GSMG Sbjct: 301 QADFSLRSVASGGETLGDDLIAWGREALGVTINEFYGQTECNLVVSSSSHCYPSVSGSMG 360 Query: 394 KPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYIT 453 + P V+I+DE G LP G G+IA++ P+ +F Y N T G F +T Sbjct: 361 RAVPGHVVQIVDEQGQVLPHGTVGNIAIRA-PDPV--MFLRYWRNEEATREKFAGDFLLT 417 Query: 454 GDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEV 513 GD G MDE GY ++ R+DD+I S+GYRIGP +E L+ HP++ +AVV D +R EV Sbjct: 418 GDLGSMDEQGYIRYLGRNDDVITSAGYRIGPAAIEECLMRHPAVRIAAVVGVKDALRTEV 477 Query: 514 VKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELR 573 VKAF+VL E LK E+Q+HV+ A ++YPR + F+ LP T +GK+ R L+ Sbjct: 478 VKAFVVLKDGVT--PDEALKAELQQHVRAQLAAHEYPRLISFVAALPTTATGKIMRKTLK 535 Query: 574 KKE 576 + + Sbjct: 536 EMD 538 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: 754 Number of extensions: 37 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: 539 Length adjustment: 36 Effective length of query: 544 Effective length of database: 503 Effective search space: 273632 Effective search space used: 273632 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