Align Putative oxidoreductase (characterized, see rationale)
to candidate WP_011385361.1 AMB_RS15030 FAD-binding protein
Query= uniprot:Q92L08 (473 letters) >lcl|NCBI__GCF_000009985.1:WP_011385361.1 AMB_RS15030 FAD-binding protein Length = 457 Score = 117 bits (293), Expect = 8e-31 Identities = 122/447 (27%), Positives = 191/447 (42%), Gaps = 56/447 (12%) Query: 42 AVLRPVTTEEVSAAVGYCVRSGIALIPQSGNTGLVSGSTPDESGSEVVVS-LDRLTRQFA 100 AV+ +TEEV+ V C G +I T L + G + VS ++R+ A Sbjct: 43 AVVFAQSTEEVAETVKACAAHGTPVIAFGTGTSLEGHVAALKGGVCIDVSGMNRVLEVRA 102 Query: 101 LDLDNRSVRVDAGFRLSELNRRLEEHGLFFPIDLGADPRIGGMIATNTGGSRFLKYGDVR 160 DLD V V G +LN L + GLFFPID GAD +GGM AT G+ ++YG +R Sbjct: 103 EDLD---VTVQPGVTRKQLNEYLRDTGLFFPIDPGADASLGGMAATRASGTNAVRYGTMR 159 Query: 161 RNTLGLKVVLADEAGTVLDLGSDLRKNNTGVDWKQIFIGTSGAFGIVTECVLNLERLPKQ 220 N L L+VVL D G V+ RK++ G D ++F+G+ G GI+TE L L+ +P+ Sbjct: 160 ENVLSLQVVLPD--GRVIRTAGRARKSSAGYDLTRLFVGSEGTLGIITELTLRLQGIPEA 217 Query: 221 TATAFL-VPASGAHVLPLLKAMEERLGAYLSAFEGMSRNAIAAA-------FAHVPALKN 272 + A P+ A V ++ ++ G ++ E + + I A P L Sbjct: 218 ISAAVCPFPSIEAAVNTVILTIQS--GVPVARIEFLDKVMIGAVNRYSKTDHREAPTLFF 275 Query: 273 PFQGGKVPDYVILAEISRTSSPREGEQPLDAVLESVLAEIWEMEEVLLADALVGPPHEIW 332 F G +S +E + ++A+ AE ++ ++W Sbjct: 276 EFHGS-------------PASVQEQAEKVEAIATEFGAEGFQWA------TGAEERTKLW 316 Query: 333 ALRH-------ALSEGVKHLGKLIAFDLSFRRGDIMAFCDHMKTEMPEKFPGVTVCDFGH 385 A RH L G + +S +A C ++TE K + GH Sbjct: 317 AARHNAYYAGVGLRPGCRAWTTDACVPIS-----RLAEC-LLETEEDLKTTPLISAIVGH 370 Query: 386 IGDGGVHFNLVVAKDSPLLADATFEQRLREWVFAVAVEQYHGSFSAEHALGRRNQAFYDL 445 +GDG H L+V P +A +R+ + A+ G+ + EH +G AF + Sbjct: 371 VGDGNFHVMLLVDPGKP--EEAAEAERINHRIVRRALAM-DGTCTGEHGVGHGKMAFLEE 427 Query: 446 YTPEKLKNMAAGLKT-----LTSPGKL 467 E L M A + + +PGK+ Sbjct: 428 EYGEALDVMRAVKRAIDPAGIMNPGKI 454 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: 492 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 473 Length of database: 457 Length adjustment: 33 Effective length of query: 440 Effective length of database: 424 Effective search space: 186560 Effective search space used: 186560 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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