Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Phaeo:GFF1551 Length = 406 Score = 584 bits (1506), Expect = e-171 Identities = 290/389 (74%), Positives = 325/389 (83%), Gaps = 2/389 (0%) Query: 7 FNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLG 66 FNW DPL LD QL+E+ERM+ SA +AQ+KL PRVL A+ +E+TDP IFREMGE+GLLG Sbjct: 18 FNWDDPLRLDDQLSEDERMIAASARSYAQEKLQPRVLNAYENEETDPEIFREMGEMGLLG 77 Query: 67 ATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLP 126 TIPEQYGG G YV YGL+AREVER+DSGYRSMMSVQSSLVM PI +G+E Q+QKYLP Sbjct: 78 TTIPEQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVMYPIYAYGSEEQRQKYLP 137 Query: 127 KLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKD 186 KL+SGEWIGCFGLTEP+ GSDP M TRA K DGGYRLTGSKMWI+N+PIADVFVVWAK Sbjct: 138 KLSSGEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKMWISNAPIADVFVVWAKS 197 Query: 187 DA--GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGP 244 +A G IRGFVLEKG +GLSAP I K LRASITGEIVMD V V ++ + P V GLKGP Sbjct: 198 EAHGGKIRGFVLEKGMKGLSAPKIANKASLRASITGEIVMDGVEVGDDALLPHVEGLKGP 257 Query: 245 FTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA 304 F CLN ARYGISWGA+GAAEACWH ARQY LDR+QFGRPLA QL Q KLA+MQTEITL Sbjct: 258 FGCLNRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPLANTQLFQLKLANMQTEITLG 317 Query: 305 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVN 364 LQ LR+GR+ DE AA E+ SI+KRN+CGKAL+IAR ARDM GGNGIS EFGV RH+VN Sbjct: 318 LQASLRVGRLMDEANAAPEMISIVKRNNCGKALEIARHARDMHGGNGISLEFGVIRHMVN 377 Query: 365 LEVVNTYEGTHDVHALILGRAQTGIQAFY 393 LE VNTYEGTHDVHALILGRAQTG+QAF+ Sbjct: 378 LETVNTYEGTHDVHALILGRAQTGLQAFF 406 Lambda K H 0.320 0.137 0.413 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: 574 Number of extensions: 19 Number of successful extensions: 2 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: 393 Length of database: 406 Length adjustment: 31 Effective length of query: 362 Effective length of database: 375 Effective search space: 135750 Effective search space used: 135750 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 (21.8 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