Align D-lactate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05735 AZOBR_RS05735 2-hydroxy-acid oxidase
Query= reanno::Phaeo:GFF2923 (444 letters) >FitnessBrowser__azobra:AZOBR_RS05735 Length = 448 Score = 518 bits (1333), Expect = e-151 Identities = 265/449 (59%), Positives = 324/449 (72%), Gaps = 11/449 (2%) Query: 1 MQTTFSEKQLRDPGTQRANEILRSCVHCGFCTATCPTYQVLGDELDSPRGRIYLIKDMLE 60 MQT F+ QL + + + ILR CVHCGFCTATCPTY +LGDELDSPRGRIY IKDMLE Sbjct: 1 MQTNFTLTQLANADYRDSEAILRKCVHCGFCTATCPTYVLLGDELDSPRGRIYQIKDMLE 60 Query: 61 NERVPDAKTVKHIDRCLSCLACMTTCPSGVHYMHLVDHARAYIDKHYNRPWSDRALRWLL 120 P VKH+DRCLSCL+CMTTCPSGV+YMHLVDHARA+I+ + RP +DRA+R LL Sbjct: 61 KGGPPTEHQVKHVDRCLSCLSCMTTCPSGVNYMHLVDHARAHIEATHARPPADRAIRDLL 120 Query: 121 ARILPYPGRFRLALIGAKLAQPFKRLVPDARLRAMLDMAPRHIPPVSRNDDPQSFAAKAP 180 AR+LP P FRLALI A +PF L+P RL A+L +AP+ +P S +D P S A P Sbjct: 121 ARVLPNPRLFRLALIAAWFGKPFAGLLP-GRLGALLALAPKSVPGPSHSDRPGSHPAVGP 179 Query: 181 RRKRVALMTGCAQKALNTDINDATIRLLTRLGCEVVVAAGAGCCGALTHHMGREEESHAT 240 RRKR AL+ GCAQ+ L IN+ATIRLL R G EVVVA GA CCGALTHHMG+ + S A Sbjct: 180 RRKRAALLVGCAQQVLAPQINEATIRLLNRQGVEVVVAKGADCCGALTHHMGKTDLSDAA 239 Query: 241 AAKNIRAWTDEIDGQGLDAIVINTSGCGTTVKDYGHMFRNDA-LAEDAARVSAIAMDISE 299 A K I AW E+DG+GLDAI++NTSGCGTTVKDY FR DA A A RV+AIA D++E Sbjct: 240 AKKTINAWIAEMDGEGLDAIIVNTSGCGTTVKDYAFQFREDAEYAPKALRVAAIARDVTE 299 Query: 300 LLMQLDLPEGE-DKETTVAYHAACSLQHGQQIKTHPKTLLKRAGFTVVEPADSHLCCGSA 358 L ++ L + +AYH+ACS+QHGQ+IK P+ LL+ AGF V E ++H+CCGSA Sbjct: 300 FLAEIGLSAPVIETGQAIAYHSACSMQHGQRIKDPPRHLLRGAGFEVKEIPEAHICCGSA 359 Query: 359 GTYNLLQPEISAELKARKVTSLEARQPDLIAAGNIGCMMQIGSATDIPILHTVELLDWAT 418 GTYN+LQPEI+ +L+ RKV ++E+ + IAAGN+GC+ QI + T +P++HTVELLDWAT Sbjct: 360 GTYNMLQPEIAVQLRDRKVRNIESTKAAAIAAGNLGCITQIATGTGLPVVHTVELLDWAT 419 Query: 419 GGPKPRAL--------VAGGPGADPRAGE 439 GGPKP AL A PGA RA E Sbjct: 420 GGPKPDALRDSPAFAGPAQAPGAAVRAAE 448 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: 647 Number of extensions: 24 Number of successful extensions: 4 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: 448 Length adjustment: 32 Effective length of query: 412 Effective length of database: 416 Effective search space: 171392 Effective search space used: 171392 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 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:
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