Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor
Query= reanno::WCS417:GFF2133 (447 letters) >FitnessBrowser__Smeli:SM_b20402 Length = 462 Score = 234 bits (597), Expect = 4e-66 Identities = 152/428 (35%), Positives = 213/428 (49%), Gaps = 33/428 (7%) Query: 5 RFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLSDCVA 64 R R A +A LVAA + R P + A A F LV++G +A L +C+A Sbjct: 2 RALRVAIGIAAVILVAAAAFFLFAWRSEI-PEDTTAAEARFAAELVAKGAQLAALGNCIA 60 Query: 65 CHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLY 124 CH++ G+ FAGGL + TP G I++TNITPD+ TGIG +S A F+RA+R GV G LY Sbjct: 61 CHTVPGRPAFAGGLALPTPFGTIYSTNITPDRETGIGGWSEAAFERAMREGVDREGSHLY 120 Query: 125 PAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTA 184 PA PY + ++S DD +ALYAF M + + +D+P+PL R +A W +F + Sbjct: 121 PAFPYEHFTRVSADDNRALYAFLMTRV-AVKAEALENDLPFPLKFRPLLAGWKLLFLDSG 179 Query: 185 TYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAP 244 P Q WNRG Y+ +G GHCG+CHTPR F + D G +GW A Sbjct: 180 EREPDPGQSDAWNRGRYLAEGLGHCGACHTPRN-PFGAEDRDR----HFGGGEAEGWQAY 234 Query: 245 SLRQDPNTGLGRWSEPQIVQFLKTG-RNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYL 303 ++ + + W E + +L+ G H V G M E N F+ D D+AAIA Y+ Sbjct: 235 AINTESKAPI-PWDEQSLAFYLRNGWHEFHGVSRGPMAEVTGN-LAFLPDSDIAAIATYV 292 Query: 304 KSLPGDP-------------------QRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGL 344 +S+ G P A Q V+A PG Y CASCH Sbjct: 293 RSIMGAPTPEREQRAAQLREAFEGQRPEQAADSQRSPVSASGSQPGEAIYLAACASCHE- 351 Query: 345 DGKGQPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEI 404 G+ QP +T+ A + +N+ L G A G A MPAFR L+D ++ Sbjct: 352 GGRRQPFGGLNFELSTAVNAPNPQNIVNVVLFGLP--PADGEASAV-MPAFRHLLNDQQV 408 Query: 405 AEVLSYVR 412 A++L+Y+R Sbjct: 409 ADLLAYMR 416 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: 617 Number of extensions: 28 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: 462 Length adjustment: 33 Effective length of query: 414 Effective length of database: 429 Effective search space: 177606 Effective search space used: 177606 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