Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate WP_011841820.1 RSPH17029_RS13510 glycolate oxidase subunit GlcF
Query= reanno::Phaeo:GFF2923 (444 letters) >NCBI__GCF_000015985.1:WP_011841820.1 Length = 433 Score = 655 bits (1691), Expect = 0.0 Identities = 312/429 (72%), Positives = 359/429 (83%) Query: 1 MQTTFSEKQLRDPGTQRANEILRSCVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLE 60 MQTTF+++QL+DPG R+NEILR+CVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLE Sbjct: 1 MQTTFTDEQLQDPGVARSNEILRACVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLE 60 Query: 61 NERVPDAKTVKHIDRCLSCLACMTTCPSGVHYMHLVDHARAYIDKHYNRPWSDRALRWLL 120 R DA+TVKHIDRCL CLACMTTCPSGVHYMHLVDHAR +I+K Y RP +R LRW + Sbjct: 61 AGRPADARTVKHIDRCLGCLACMTTCPSGVHYMHLVDHARDHIEKTYRRPLFERLLRWTV 120 Query: 121 ARILPYPGRFRLALIGAKLAQPFKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAP 180 A++LPYP RFR AL A+L +PF LVPDARL+AML +AP H+P S ND PQ F A P Sbjct: 121 AQLLPYPARFRAALRLAQLGRPFAGLVPDARLKAMLALAPHHVPKPSPNDRPQVFEATGP 180 Query: 181 RRKRVALMTGCAQKALNTDINDATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHAT 240 +R RVAL+TGCAQ+AL+TDINDATIRLL R+GCEVV+ G GCCGALTHHMGR E+SH Sbjct: 181 KRMRVALLTGCAQRALDTDINDATIRLLRRMGCEVVIPKGMGCCGALTHHMGRAEQSHGL 240 Query: 241 AAKNIRAWTDEIDGQGLDAIVINTSGCGTTVKDYGHMFRNDALAEDAARVSAIAMDISEL 300 AA NIR+W E +GLDAIVINTSGCGTT+KDYGH+FRND LA +AA VSA+A+D++EL Sbjct: 241 AATNIRSWMSEKRARGLDAIVINTSGCGTTIKDYGHIFRNDPLAAEAAEVSALALDVTEL 300 Query: 301 LMQLDLPEGEDKETTVAYHAACSLQHGQQIKTHPKTLLKRAGFTVVEPADSHLCCGSAGT 360 L +L LPEG K VAYH+ACSLQHGQ+I+ PK LL RAGF V EPAD HLCCGSAGT Sbjct: 301 LERLGLPEGVPKGLRVAYHSACSLQHGQRIRQAPKELLARAGFEVTEPADPHLCCGSAGT 360 Query: 361 YNLLQPEISAELKARKVTSLEARQPDLIAAGNIGCMMQIGSATDIPILHTVELLDWATGG 420 YNLL PEISAELKARKV +LEAR+PD+++AGNIGC+MQIGS +P++HTVELLDWATGG Sbjct: 361 YNLLHPEISAELKARKVATLEARKPDVVSAGNIGCIMQIGSGMGVPVVHTVELLDWATGG 420 Query: 421 PKPRALVAG 429 PKPR L G Sbjct: 421 PKPRRLELG 429 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: 694 Number of extensions: 25 Number of successful extensions: 1 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: 444 Length of database: 433 Length adjustment: 32 Effective length of query: 412 Effective length of database: 401 Effective search space: 165212 Effective search space used: 165212 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 Apr 10 2024. 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