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_011426974.1 RHE_RS19290 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_000092045.1:WP_011426974.1 Length = 550 Score = 251 bits (642), Expect = 4e-71 Identities = 180/557 (32%), Positives = 275/557 (49%), Gaps = 38/557 (6%) Query: 33 NFSNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFE 92 +F Y + +DF IPE FN + V D+W + L + NG+ L ++ Sbjct: 5 SFDRYGDLYRDFSWRIPEDFNIGRAVSDEWAARDPERVCLEH-----FSPNGDHLSLTYG 59 Query: 93 ELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKD 152 EL S FAN L + ++RGDRV +++P+ E +A+VA + G + +P + Sbjct: 60 ELSAASSMFANALA-SLGIKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEA 118 Query: 153 ILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKYAS-- 210 + YRL+ S A IIT+D V + + L + VS + + + +A Sbjct: 119 LEYRLRISGAAAIITNDFGLDRVRQIRDRLPELRHVISVSDAA--------DALSFADLI 170 Query: 211 DSHTCV----DTKHDEMMAIYFTSGTTGPPKMIGHTHSSF-----GLGLSVNGRFWLDLI 261 SH V T D+ + FTSGTTGPPK H H G+ + G + Sbjct: 171 ASHASVFEGEKTTPDDAALMIFTSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKV--- 227 Query: 262 ASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAP 321 D +W SD WA +++ G V + +F++ + + +++ + P Sbjct: 228 -GDKVWTPSDWAWAGGLLNALLPSLLLGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPP 286 Query: 322 TAYRML--VQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLIC 379 TA R++ V + S Y L+ SAGE + E + R+ G+ + E YGQTE + Sbjct: 287 TALRLMRSVSDPRSKYDL-VLRTVGSAGEALGRETYDWARRTLGITVNEFYGQTECNFVL 345 Query: 380 GNFKGMKI-KPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDN 438 + + K G++G+ P V I+ E G LP G+ G IA+ P+ +F Y ++ Sbjct: 346 SSSAAFGVTKAGAIGRAVPGHRVAIVSEAGDELPAGESGQIAI-ASPDPV--MFLGYWND 402 Query: 439 PSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIA 498 + T + +TGD G DEDGY F R DD+I SSGYRIGP E+E L HP++ Sbjct: 403 AAATERKFLHGWLLTGDIGRQDEDGYVTFEGRDDDVITSSGYRIGPAEIEDCLTGHPAVQ 462 Query: 499 ESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEE 558 +A V PD +R E+VKA+IVL+P + E L EI+E VK + ++YPR+VEF+E Sbjct: 463 LAAAVGKPDVVRTEIVKAYIVLSPGHS--PSEALAAEIREWVKMRLSMHEYPREVEFVES 520 Query: 559 LPKTVSGKVKRNELRKK 575 LP T +GKV R LR+K Sbjct: 521 LPLTTTGKVIRRLLREK 537 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: 766 Number of extensions: 35 Number of successful extensions: 8 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: 550 Length adjustment: 36 Effective length of query: 544 Effective length of database: 514 Effective search space: 279616 Effective search space used: 279616 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 Apr 09 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