Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor
Query= SwissProt::O34215 (441 letters) >FitnessBrowser__Smeli:SM_b20402 Length = 462 Score = 228 bits (580), Expect = 4e-64 Identities = 149/399 (37%), Positives = 210/399 (52%), Gaps = 52/399 (13%) Query: 27 LVKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDDF 86 LV +G LA G+C+ACH+V G FAGGL + TP GTIYSTNITPD+ TGIG +S F Sbjct: 45 LVAKGAQLAALGNCIACHTVPGRPAFAGGLALPTPFGTIYSTNITPDRETGIGGWSEAAF 104 Query: 87 QKAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPLS 146 ++A+R GV + G LYPA PY + VS +D +ALYA+ M VA A+A ++D+P+PL Sbjct: 105 ERAMREGVDREGSHLYPAFPYEHFTRVSADDNRALYAFLMTRVAVKAEA-LENDLPFPLK 163 Query: 147 MRWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALSN 206 R LA W+ +F D +P + RGRYL EGLGHCGACHTPR+ Sbjct: 164 FRPLLAGWKLLFL-DSGEREPDPGQSDAWNRGRYLAEGLGHCGACHTPRN------PFGA 216 Query: 207 DGAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGRNDHTAAFGGMTDVV 266 + + G A +GW A + +++ + W E L +LR G ++ G V Sbjct: 217 EDRDRHFGGGEA--EGWQAYAINTESKAPI-PWDEQSLAFYLRNGWHEFHGVSRGPMAEV 273 Query: 267 EHSLQHLSDDDITAIARYLKSL----------------GAKDASQTVFTQDDQVAKALWK 310 +L L D DI AIA Y++S+ A + + D Q + Sbjct: 274 TGNLAFLPDSDIAAIATYVRSIMGAPTPEREQRAAQLREAFEGQRPEQAADSQRSPVSAS 333 Query: 311 GDDSQTGASVYVDSCAACHKTDGSRLSALLPGAAWQPGG---------AGEPDPTSLIHI 361 G SQ G ++Y+ +CA+CH+ G QP G P+P +++++ Sbjct: 334 G--SQPGEAIYLAACASCHE-----------GGRRQPFGGLNFELSTAVNAPNPQNIVNV 380 Query: 362 VLTGGTLPGVQGAPTAITMPAFGWRLNDQQVADVVNFIR 400 VL G LP G +A+ MPAF LNDQQVAD++ ++R Sbjct: 381 VLFG--LPPADGEASAV-MPAFRHLLNDQQVADLLAYMR 416 Lambda K H 0.317 0.133 0.409 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: 590 Number of extensions: 36 Number of successful extensions: 9 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: 462 Length adjustment: 33 Effective length of query: 408 Effective length of database: 429 Effective search space: 175032 Effective search space used: 175032 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 (21.6 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