Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate N515DRAFT_0703 N515DRAFT_0703 Cytochrome c
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Dyella79:N515DRAFT_0703 Length = 429 Score = 292 bits (747), Expect = 2e-83 Identities = 166/428 (38%), Positives = 227/428 (53%), Gaps = 15/428 (3%) Query: 13 LALPCLVAAGLLAWYVTR--EPATPFEQEQ--AGATFEPALVSRGEYVARLSDCVACHSL 68 +A+ L+ GL W R +P+ P + A A +PAL+++GEY+ + DC +CH+ Sbjct: 8 IAVVVLLGLGLAGWLFLRGGQPSVPRSASRVDAAALKDPALIAKGEYLTLVGDCASCHTG 67 Query: 69 AGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLYPAMP 128 G A FAGG + TP G I A N+TPD+ TG+G +S F +A+ GV G+ LYPA P Sbjct: 68 QGGARFAGGRVVGTPFGDIPAPNLTPDRETGLGEWSFEAFRQALHSGVDRHGQFLYPAFP 127 Query: 129 YPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTATYAA 188 Y SY K+S DD A++A ++Q + P Q + +P N+R + W ++ Y A Sbjct: 128 YTSYTKVSRDDALAIFA-YLQSLPPLKQAAKQPGLGFPYNVRNTLKAWRALYFREGEYVA 186 Query: 189 KPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALL--DGWYAPSL 246 + WNRGAY+VQG GHC CH R +F D++ L+G + WYAP L Sbjct: 187 DSTKSPEWNRGAYLVQGLGHCNECHVERD-SFGGMRSDQS----LSGGQIPVQNWYAPDL 241 Query: 247 RQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYLKSL 306 N GL WSE I LKTG++A +G M E STQ + D DL AIA YL+SL Sbjct: 242 STQANGGLAGWSERDIADLLKTGQSAKGAAFGPMAEVVARSTQHLNDADLHAIATYLQSL 301 Query: 307 PGDPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGATSALAKE 366 P P+ P + GA YA RCA CHG DG+G PPL+G +S Sbjct: 302 PARPRVSYEPSLLDTKPMLDQ--GAKVYAERCADCHGRDGQGVAGVYPPLSGNSSVNEPT 359 Query: 367 SASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGGAVDANA 426 +AI + L G G P Y MP F +QL+D ++A V++Y+R +WGN V Sbjct: 360 GINAIRVVLLGGFAPSTQGNPRPYSMPPFAQQLNDADVAAVVTYIRQSWGNQAPLVQERD 419 Query: 427 VGKLRGHT 434 V K R HT Sbjct: 420 VIKYR-HT 426 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: 630 Number of extensions: 36 Number of successful extensions: 7 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: 429 Length adjustment: 32 Effective length of query: 415 Effective length of database: 397 Effective search space: 164755 Effective search space used: 164755 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