Align Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale)
to candidate AO353_27065 AO353_27065 cytochrome C oxidase Cbb3
Query= uniprot:A4PIB1 (441 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27065 Length = 415 Score = 240 bits (613), Expect = 5e-68 Identities = 152/421 (36%), Positives = 222/421 (52%), Gaps = 23/421 (5%) Query: 18 AICVVQSSGAYAADADLIKRGAYVAVLGDCEACHTAHDGKSLAGGLALQSPLGAIYSTNI 77 A+ ++ A AAD IKRG Y+A DC ACHTA G AGGL + SP G IY TNI Sbjct: 15 AVSLMAIQQAQAADQQQIKRGEYLARAADCMACHTAPGGAPYAGGLPIVSPFGTIYGTNI 74 Query: 78 TPDRDTGIGTWSYEDFARLMRRGIRKDGSSVYPAMPYPSYSKMTDEDLQALYAYLTQGVA 137 TPD+D GIG +S ++F + G R+DG+++YPAMPY SY M ED A++AYL Q VA Sbjct: 75 TPDKDHGIGQYSDDEFFAALTEGKRRDGANLYPAMPYTSYHLMPREDSDAIHAYL-QTVA 133 Query: 138 PVSLKNRAPDIPWLLSARWPLAIWRLLFAPSPAPPLPSAPHDDTSDALVERGRYLVEGPG 197 P++ + + + R L W +L+ + P + S+ +RG+YLV+ G Sbjct: 134 PINRAAPVTRLSFPFNVRLGLMGWNMLYGKD----VKLTPAEGKSEDW-KRGQYLVDVLG 188 Query: 198 HCGSCHTPRNFVLAEKVQTAADGPKYLSGGFIVDNWVAPSLRSDDAGGLVGWTPEDIVAF 257 HCG CHTPR + A K L+GG +++ ++APSL ++D GWT +D+ +F Sbjct: 189 HCGECHTPRG------LPGAMQQDKRLTGG-LLNGYLAPSLLANDLAAR-GWTHQDLSSF 240 Query: 258 LKTGRNRHGATFGAMNGVITHSTSLTDDHDLAAIAAFLKTLG-PPPGVSVQAFHYDDTVS 316 LK G + G F M V +ST ++ DLA++A FL LG PPP V + D ++ Sbjct: 241 LKHGMSAQGTMFNEMFPVFHNSTQNLNEPDLASMATFL--LGDPPPQARVLSEVPLDKMT 298 Query: 317 RQLFAGKMPSEGARIYVDRCAACHRTDGHGYPGVFPPLAGNPVLQGPDATSAAHIILSGG 376 G+ Y++ CA CH +G G P + + GN L+ D + +I G Sbjct: 299 ESARRGRQD------YLNVCAGCHGVNGEGKPHIAVAMQGNTTLRLEDPRNLLRVIEDGI 352 Query: 377 RLPGVAAAPSSLVMGSYRDVLDNQQIADLVTFLGQSWGNHGAAMTASQVAKIRQATTDEK 436 A M + D L NQQ+ DL+++L Q+WG A + Q+ +++ E Sbjct: 353 GEQKFAGFERMQPMPGFADKLSNQQMTDLISYLRQAWGGQPADLLIGQIEQLKADAPVEH 412 Query: 437 K 437 K Sbjct: 413 K 413 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: 523 Number of extensions: 26 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: 415 Length adjustment: 32 Effective length of query: 409 Effective length of database: 383 Effective search space: 156647 Effective search space used: 156647 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: 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