Align Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale)
to candidate RR42_RS21615 RR42_RS21615 alcohol dehydrogenase
Query= uniprot:A4PIB1 (441 letters) >FitnessBrowser__Cup4G11:RR42_RS21615 Length = 1000 Score = 230 bits (586), Expect = 2e-64 Identities = 154/395 (38%), Positives = 209/395 (52%), Gaps = 21/395 (5%) Query: 19 ICVVQSSGAYAADADLIKRGAYVAVLGDCEACHTAHDGKSLAGGLALQSPLGAIYSTNIT 78 I V GA A I+RG VA GDC CHTA +G AGGLAL +P G IYSTNIT Sbjct: 588 IAPVAPPGAGFYSAATIERGRLVAAAGDCAVCHTAPNGARNAGGLALDTPFGTIYSTNIT 647 Query: 79 PDRDTGIGTWSYEDFARLMRRGIRKDGSSVYPAMPYPSYSKMTDEDLQALYAYLTQGVAP 138 PD +TGIG WSY F R MR+GI +DG +YPA PY +++K +D DLQALYAYL P Sbjct: 648 PDVETGIGNWSYAAFERAMRQGIHRDGRHLYPAFPYTAFAKTSDGDLQALYAYL-MAAEP 706 Query: 139 VSLKNRAPDIPWLLSARWPLAIWRLLFAPSPAPPLPSAPHDDTSDALVERGRYLVEGPGH 198 V K + + + R +A W LLF SP P D A RG YL EG GH Sbjct: 707 VRAKAPETALAFPYNLRPLMAGWNLLF-HSPKP----FEADPARSAQWNRGAYLAEGLGH 761 Query: 199 CGSCHTPRNFVLAEKVQTAADGPKYLSGGFIVDNWVAPSLRSDDAGGLVGWTPEDIVAFL 258 C +CH+PRN + AE+ G +YL GG + W AP+L + V WT + + ++L Sbjct: 762 CSACHSPRNALGAEQ-----GGRRYLGGG-EAEGWEAPAL-GKLSHAPVPWTEQALFSYL 814 Query: 259 KTG-RNRHGATFGAMNGVITHSTSLTDDHDLAAIAAFLKTLG-PPPGVSVQAFHYDDTVS 316 +TG HGA G M VI +L + D+ AIA ++ + G P ++ + Sbjct: 815 RTGYAPHHGAAAGPMAPVI-EELALLPEEDVRAIAHYVASFGDAQPDAALASAQARQLEQ 873 Query: 317 RQLFAGK-MPSEGARIYVDRCAACHRTD-GHGYPGVFPPLAGNPVLQGPDATSAAHIILS 374 R A + + AR+Y + CA CH++D G G+ P LA N L G + ++L Sbjct: 874 RSADAARTLGGPAARLYQNACAVCHQSDQGIRQFGIKPSLALNTNLHGDKPDNLIRVLLD 933 Query: 375 GGRLPGVAAAPSSLVMGSYRDVLDNQQIADLVTFL 409 G PG + M ++ + LD++Q+ LV +L Sbjct: 934 GIPTPGTSDLG---YMPAFGESLDDRQLTQLVHYL 965 Lambda K H 0.318 0.135 0.420 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: 1272 Number of extensions: 83 Number of successful extensions: 6 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: 441 Length of database: 1000 Length adjustment: 38 Effective length of query: 403 Effective length of database: 962 Effective search space: 387686 Effective search space used: 387686 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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