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_RS04625 HSERO_RS04625 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__HerbieS:HSERO_RS04625 Length = 556 Score = 259 bits (662), Expect = 2e-73 Identities = 170/509 (33%), Positives = 271/509 (53%), Gaps = 18/509 (3%) Query: 74 NPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVA 133 N A ++ +GE ++SF ++ ++ + AN+L + +Q G V +LP+ PE + Sbjct: 52 NIALEFVSLHGEHQQYSFAQVRSMAARVANLLRQQ-GIQPGQIVAGMLPRTPELLATVLG 110 Query: 134 CLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQ 193 LR G V P T K I +RL S A I+T+ +D +A C + + + Sbjct: 111 TLRAGAVYQPLFTAFGPKAIEHRLALSGASLIVTNVANRDKLDEIA-NCPQVCTVRESND 169 Query: 194 HSREGWGNLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVN 253 R G + + + SD V ++M + TSGTTG K + S+ SV Sbjct: 170 PLRAGDIDFRAAVDAQSDDFAPVLRSGADLMLMMSTSGTTGAAKGVPVPLSALQ-AFSVY 228 Query: 254 GRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFP 313 R + L+ D WN +D GWA + ++ P G + + F + +T+ + Sbjct: 229 MREAVGLLPQDKFWNMADPGWAYGLYYAIIGPLAIGHGITFNEAA-FTVSGTYETIRRLG 287 Query: 314 ITVFCSAPTAYRMLVQ--NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYG 371 IT APTAYRM++ + ++ L+ SAGEP+N EV+ + + I++ YG Sbjct: 288 ITSLAGAPTAYRMMMAAGEEAAASVKGRLRAVSSAGEPLNAEVVRWFASALDVPIHDHYG 347 Query: 372 QTETVLICGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPF 429 QTE ++ N ++ + PGS G P + V +LDEN L Q G++A+ + P Sbjct: 348 QTELGMVVNNHHALRHEVVPGSAGFAMPGYRVVVLDENHQELGANQPGELAIDIA-RSPL 406 Query: 430 GLFTHY--VDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEV 487 F+ Y D P+ + +Y TGD ++ +G F+ RSDD+I S+GYRIGPF+V Sbjct: 407 YWFSGYWKQDTPA-----IAHGYYSTGDNVELEPNGSISFIGRSDDVITSAGYRIGPFDV 461 Query: 488 ESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPY 547 ESAL+EHP++A+ AV+ PDP R E+VKAF+VL+ +K+ D L++++ +HVK+ + + Sbjct: 462 ESALLEHPAVADVAVIGLPDPERTEIVKAFVVLSDQFKASD--ALREQLAQHVKRRLSAH 519 Query: 548 KYPRKVEFIEELPKTVSGKVKRNELRKKE 576 YPR +EF++ LPKT SGK++R LRK E Sbjct: 520 AYPRAIEFLDALPKTPSGKLQRFVLRKME 548 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: 744 Number of extensions: 40 Number of successful extensions: 9 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: 556 Length adjustment: 36 Effective length of query: 544 Effective length of database: 520 Effective search space: 282880 Effective search space used: 282880 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