Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_02128 CCNA_02128 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20676 (396 letters) >FitnessBrowser__Caulo:CCNA_02128 Length = 401 Score = 271 bits (693), Expect = 2e-77 Identities = 168/399 (42%), Positives = 228/399 (57%), Gaps = 25/399 (6%) Query: 11 AFRDEVRQFFKDNVPAKTRQKLIE------GRHNT--KEEMVEWYRILNKKGWAVTHWPK 62 AFR + R + + N P + E GR + W + ++GW WPK Sbjct: 11 AFRADTRAWLEANYPKSLNAPMGEDEAPWGGRKMVWKNPDAKLWLDRMAERGWTAPMWPK 70 Query: 63 EYGGTGWSSVQHYIFNEELQAAPA-PQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANVD 121 EYGG G S Q+ + +EL+ A P ++FGV M+GPV+ + +EEQK+RFLP I + Sbjct: 71 EYGGGGLSKAQNKVLEQELRRLKARPALMSFGVWMLGPVLLEYATEEQKQRFLPAIVRGE 130 Query: 122 DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLAQHADWIFCLCRTDPAAKK 181 WCQG+SEPG+GSDLASL+TK E KGD ++INGQK WT+ A ADWIFCL RTD +KK Sbjct: 131 TRWCQGYSEPGAGSDLASLQTKCEDKGDHYLINGQKVWTSYADQADWIFCLVRTD-TSKK 189 Query: 182 QEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYAKFLL 241 EGISF+L DM + G+ RPI+ I G E FFD+V+VP E LVG+ N GWD AK LL Sbjct: 190 HEGISFVLFDMTSPGVEARPIKLISGSSPFCETFFDNVKVPKEQLVGKLNGGWDIAKRLL 249 Query: 242 GNERTGIARVGMSKERIRRIKQLAAQ---VESGGKPVIEDPKFRDKLAAVEIELKALELT 298 ER I+ G + + A + V+S G+ I D FR +LAA ++ A LT Sbjct: 250 QYERQNISASGFGGGGGLSVVEAAKKELGVDSEGR--IADGDFRARLAAHSMDAHAFMLT 307 Query: 299 QLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDDSNET 358 R A E K G G P+ A S++K +++ Q TELL+E +G + G+D S E Sbjct: 308 VRRAEA-ESKQGSG-PSAAVSIIKYAAAKMNQERTELLVEALGLQGLGWS--GEDFSAEE 363 Query: 359 MDWTAQIAP-GYFNNRKVSIYGGSNEIQRNIICKAVLGL 396 + AP + SI GG++E+ N++ K VLGL Sbjct: 364 L-----AAPRAMLRAKGNSIEGGTSEVNLNVVAKRVLGL 397 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: 435 Number of extensions: 28 Number of successful extensions: 5 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: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 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