Align Putative oxidoreductase (characterized, see rationale)
to candidate WP_061534524.1 CAter10_RS18180 FAD-binding oxidoreductase
Query= uniprot:Q92L08 (473 letters) >NCBI__GCF_001584165.1:WP_061534524.1 Length = 472 Score = 367 bits (942), Expect = e-106 Identities = 195/464 (42%), Positives = 286/464 (61%), Gaps = 18/464 (3%) Query: 10 LTKLLGDKGVVTRREDMEAYEAGARYDRGRAAAVLRPVTTEEVSAAVGYCVRSGIALIPQ 69 + LLG +G + + E + YE GARY G++ + RP +E + + C R I ++PQ Sbjct: 11 IADLLGPQGCLLQPEQRQLYEKGARYGDGKSLCIARPANVDEAAELMRLCARDKIRIVPQ 70 Query: 70 SGNTGLVSGSTPDESGSEVVVSLDRLTRQFALDLDNRSVRVDAGFRLSELNRRLEEHGLF 129 NTGLV ++PD SG +V++S++R+ +D +R V+ AG RLSELN+ LE+H L+ Sbjct: 71 GANTGLVGAASPDRSGLDVLLSMERIKGVIDIDPVDRVVQAYAGTRLSELNQALEKHDLY 130 Query: 130 FPIDLGADPRIGGMIATNTGGSRFLKYGDVRRNTLGLKVVLADEAGTVLDLGSDLRKNNT 189 FPIDLGADP +GGM+A NTGG+R ++YGDVR NTLGL+ +L D G LDL + LRKNNT Sbjct: 131 FPIDLGADPSLGGMLAANTGGARLIRYGDVRHNTLGLEALLIDPPGERLDLTNRLRKNNT 190 Query: 190 GVDWKQIFIGTSGAFGIVTECVLNLERLPKQTATAFLVPASGAHVLPLLKAMEERLGAYL 249 G DWKQ FIGT GA+G++T+ VL + P+Q+ATA + PAS LL+ +E +L Sbjct: 191 GPDWKQCFIGTGGAYGVITQVVLQVHPRPQQSATALVAPASMEAAALLLRDVERNFADFL 250 Query: 250 SAFEGMSRNAIAAAFAHVPALKNPFQGGKVPDYVILAEISRTSSPREGEQPLD----AVL 305 SAFEG+S+NA+ + HVP + PF+ +P Y L E+S ++ PR + L+ A L Sbjct: 251 SAFEGISQNALQSVLQHVPGIAAPFE--PLPPYAFLIELS-SARPRSADFDLEKLFGAWL 307 Query: 306 ESVLAEIWEMEEVLLADALVGPPHEIWALRHALSEGVKHLGKLIAFDLSFRRGDIMAFCD 365 ES + L+ DA++ P +W +RHA+S+ V+ GK++AFD+S R + F Sbjct: 308 ESCFGD-------LILDAVIDKPEVLWRIRHAISDSVRQEGKVVAFDISVPRSSLGQFRQ 360 Query: 366 HMKTEMPEKFPGVTVCDFGHIGDGGVHFNLVVAKDSPLLAD--ATFEQRLREWVFAVAVE 423 + + G+ + DFGH GDGG+HFNL + + L+AD LR+ ++ +AV Sbjct: 361 EAAALLEQSHAGIKLFDFGHWGDGGLHFNLAIPEQ--LIADFPPLRINALRQEIYDLAVL 418 Query: 424 QYHGSFSAEHALGRRNQAFYDLYTPEKLKNMAAGLKTLTSPGKL 467 +Y GSFSAEH +G NQ FY+ YT +A ++ + P +L Sbjct: 419 KYKGSFSAEHGVGPFNQQFYERYTTPAQLALATRMQNVFDPERL 462 Lambda K H 0.320 0.137 0.402 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: 572 Number of extensions: 24 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: 473 Length of database: 472 Length adjustment: 33 Effective length of query: 440 Effective length of database: 439 Effective search space: 193160 Effective search space used: 193160 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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