Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_084610247.1 A3GO_RS0118680 (Fe-S)-binding protein
Query= reanno::Phaeo:GFF2923 (444 letters) >NCBI__GCF_000428045.1:WP_084610247.1 Length = 412 Score = 192 bits (487), Expect = 2e-53 Identities = 133/401 (33%), Positives = 193/401 (48%), Gaps = 37/401 (9%) Query: 25 CVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLENERVPDAKTVKHIDRCLSCLACMT 84 CV CG C CPTY ++ DE DSPRGRI LI+ + + + +H+DRCL CLAC Sbjct: 32 CVKCGICLPHCPTYSLMRDEGDSPRGRISLIQGIASGA-LDSKQASRHLDRCLGCLACQA 90 Query: 85 TCPSGVHYMHLVDHARAYIDKHYNRPWSDRALRWLLARILPYPG--RFRLALIGAKLAQP 142 CPS V+Y L+D R DK + R L+ R LPY G R L L +P Sbjct: 91 VCPSAVNYGQLIDGFRTTQDKSRRQ----RLTHHLITR-LPYRGWGRIGLWLYRHSGIRP 145 Query: 143 FKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAPRRKRVALMTGCAQKALNTDIND 202 R + +R R + + P N Q ++ P++ RV L TGCA + + D Sbjct: 146 LLRTLGGSRFRRLDALLPDQASVGRWN---QHYSPVTPKQGRVGLFTGCAGRISDRQALD 202 Query: 203 ATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHATAAKNIRAWTDEIDGQGLDAIVI 262 A + +LTRLG EV++ GCCGA+ H G + A A N +A+ + +GLDAIV Sbjct: 203 AAVAVLTRLGYEVIIPGDQGCCGAMHQHSGDPVTAAAMAINNQQAFGE----KGLDAIVY 258 Query: 263 NTSGCGTTVKDYGHMFRNDALAEDAARVSAIAMDISELLMQLDLPEG---EDKETTVAYH 319 SGCGT + + ++S+ L PE + V H Sbjct: 259 LASGCGTQL--------------IKQPFTTPVYEVSQFLNHCCWPEDSVLSPMDCAVGLH 304 Query: 320 AACSLQHGQQIKTHPKTLLKRAGFTVVEPADSHLCCGSAGTYNLLQPEISAELKARKVTS 379 + C+L+H ++ P+ LL R + D CCG+AG+Y L QP+++ L AR + Sbjct: 305 SPCTLKHQLKLADEPEKLLLRIPGIRLVRLDRIECCGAAGSYLLEQPDMADALGARAIQQ 364 Query: 380 LEARQPDLIAAGNIGCMMQIG---SATDIPI--LHTVELLD 415 + ++ +A N GC +Q T PI +H VEL++ Sbjct: 365 VPVQELQYLATSNSGCALQFTREIRKTGYPIKTVHPVELIN 405 Lambda K H 0.321 0.135 0.419 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: 488 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 412 Length adjustment: 32 Effective length of query: 412 Effective length of database: 380 Effective search space: 156560 Effective search space used: 156560 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 (21.9 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