Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate SMc00086 SMc00086 diheme cytochrome C-type signal peptide protein
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Smeli:SMc00086 Length = 304 Score = 150 bits (379), Expect = 5e-41 Identities = 99/297 (33%), Positives = 145/297 (48%), Gaps = 17/297 (5%) Query: 18 LVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVACHSLAG-----KA 72 +VA LAW++T+ ++ P L + GE + CV+CHS G + Sbjct: 16 VVAGASLAWWLTKPDR--WDAAHWEGLGGPDLAN-GEQIFWAGGCVSCHSAPGAKDDQRL 72 Query: 73 PFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMPYPSY 132 GG + +P G + NI+PD++ GIG ++LA+F A+ GV G LYP+ PY SY Sbjct: 73 VLTGGRTLKSPFGTFYPPNISPDETVGIGNWTLAEFGDAMTRGVGKDGEHLYPSFPYGSY 132 Query: 133 VKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAAKPDQ 192 ++++ D+ L+ FMQ + ++ P D+ +P N+R + W ++ Sbjct: 133 IRMTAKDVNDLWG-FMQTLPKSSNATPPHDLAFPYNVRLALGAWKLLYLSDEPRTQVNTA 191 Query: 193 DALWNRGAYIVQGPGHCGSCHTPR-GLAFNEKALDEAGAPFLAGALLDGWYAPSLRQDPN 251 D RG Y+V+GPGHCG CHTPR L E+ AGAP G PS + Sbjct: 192 DTKLARGQYLVEGPGHCGECHTPRDALGGFEEDRWLAGAPNPEGEGRIPDITPS-----S 246 Query: 252 TGLGRWSEPQIVQFLKTGRNA-HAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSLP 307 +G WS I +L+TG V GSM E N + + D AIA YLK+LP Sbjct: 247 KSIGDWSASDIASYLETGFTPDFDTVGGSMVEVQKNMAE-LPASDRDAIAAYLKALP 302 Lambda K H 0.318 0.133 0.423 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: 496 Number of extensions: 30 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: 447 Length of database: 304 Length adjustment: 30 Effective length of query: 417 Effective length of database: 274 Effective search space: 114258 Effective search space used: 114258 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: 49 (23.5 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