Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_033102282.1 JG50_RS0116910 FAD-binding protein
Query= reanno::psRCH2:GFF3772 (499 letters) >NCBI__GCF_000763315.1:WP_033102282.1 Length = 470 Score = 340 bits (871), Expect = 8e-98 Identities = 169/419 (40%), Positives = 260/419 (62%), Gaps = 1/419 (0%) Query: 56 PLLVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEV 115 P +VV P+ ++ ++KL ++ +PV RG GT LSGG LP+ GI+L M R NK+L + Sbjct: 41 PDVVVFPQSATEIAEIMKLANREQIPVTPRGGGTSLSGGPLPVAGGIVLAMTRMNKLLRI 100 Query: 116 DPAGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLT 175 D A V+PG+ + + A L+Y PDPSS +IGGN+AEN+GG H LKYG+T Sbjct: 101 DRDNLIAFVEPGITTAELQREAEKAGLFYPPDPSSSNVSTIGGNLAENSGGPHGLKYGVT 160 Query: 176 VHNLLKVDILTVEGERMTLGSDALDS-PGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVA 234 H ++ ++++T +GE + G + + G+DL +L GSEG LGI+T+ ++L+PKP Sbjct: 161 KHYVIGLEVVTPQGEIIRTGGMTVKNVTGYDLTSLIVGSEGTLGIITKAVLRLIPKPPAR 220 Query: 235 KVLLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCE 294 K L+A FD + +GRA+ I+ GI+P LEMMD SIRA E++ +G P+DA AILL E Sbjct: 221 KALMAIFDEIVDSGRAISGILKNGILPAKLEMMDQASIRAVENYQPSGLPLDAAAILLLE 280 Query: 295 LDGVEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCM 354 +DG A V ++ + +++ + A EVRLA DEAER W RK PA+ ++ P Sbjct: 281 VDGHPAAVDEEIRKAAQICRQYAAREVRLAADEAERAELWKARKLVSPAISQVKPTKISE 340 Query: 355 DGTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGG 414 D T+PR ++P +L+ + + E++ L + HAGDGN+HP I+ D+ E++R E+ Sbjct: 341 DATVPRSKIPEMLERLRQIREKYQLHLVVFGHAGDGNLHPNIIADSRDRDEMKRVEEAVA 400 Query: 415 KILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIP 473 +I + V++GG+++GEHG+G K M + + L + +K A+DP+ +LNP K P Sbjct: 401 EIFKAAVELGGTLSGEHGIGTMKPAFMEMELGSAGLDMMRRIKQAWDPNNILNPFKIFP 459 Lambda K H 0.320 0.140 0.412 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: 562 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: 499 Length of database: 470 Length adjustment: 34 Effective length of query: 465 Effective length of database: 436 Effective search space: 202740 Effective search space used: 202740 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: 52 (24.6 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