Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate GFF53 HP15_53 acyl-CoA dehydrogenase domain protein
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Marino:GFF53 Length = 383 Score = 176 bits (447), Expect = 8e-49 Identities = 128/393 (32%), Positives = 196/393 (49%), Gaps = 26/393 (6%) Query: 7 KEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHWPKEYGG 66 +E R EV+ F K + T L + H+ E+ R L KGW P +YGG Sbjct: 13 QEAELLRSEVQSFLKSEL---TDYPLSDRAHSWMGFDAEFSRKLGAKGWLGMSLPIQYGG 69 Query: 67 TGWSSVQHYIFNEELQAAPAPQPLAFGVS-MVGPVIYTFGSEEQKKRFLPRIANVDDWWC 125 S Y+ EEL AA AP + GP+I FG+ EQK++FLP I + ++C Sbjct: 70 AEASPFARYVVIEELLAAGAPVSAHWIADRQSGPLIQRFGTAEQKEKFLPSICKGESFFC 129 Query: 126 QGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAK--KQE 183 G SEP SGSDLAS+KT A++ + W++NGQK WTT A + ++ L RT + + Sbjct: 130 IGMSEPDSGSDLASIKTNAKRTDNGWVLNGQKVWTTNAHLSHYMIALVRTGDREETGRHG 189 Query: 184 GISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLLGN 243 G+S ++D+ G+TVR I + GG NEVFFD+V + + L+G+E GW L Sbjct: 190 GMSQFIIDLSLPGVTVRAIPDLTGGEHFNEVFFDNVALEKDALIGEEGAGWQQVTAELAF 249 Query: 244 ERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALELTQLRVV 303 ER+G R S + AA G P + ++ A + L+ + L+ + + Sbjct: 250 ERSGPERFLSSIALV-----YAALDVIGTNPDALQSRDIGRITARLLTLRDMSLSVTQQL 304 Query: 304 ADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNETMDWTA 363 +D G++ P A+S +K G+ +Q E+L +I + G + + + + Sbjct: 305 SD-GEN----PAWAASCVKDLGNAFEQEIPEILQLLI---EQQPQIDGGSEYSRVLAYLT 356 Query: 364 QIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 Q+AP + S+ GG+ EI R II + LGL Sbjct: 357 QMAPSF------SLRGGTREILRGIIARG-LGL 382 Lambda K H 0.317 0.135 0.411 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: 362 Number of extensions: 17 Number of successful extensions: 3 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: 396 Length of database: 383 Length adjustment: 30 Effective length of query: 366 Effective length of database: 353 Effective search space: 129198 Effective search space used: 129198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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