Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate PP_2479 PP_2479 Cytochrome c family protein
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Putida:PP_2479 Length = 407 Score = 237 bits (604), Expect = 6e-67 Identities = 148/419 (35%), Positives = 219/419 (52%), Gaps = 20/419 (4%) Query: 19 KLAAAIGLMAVSFGAAHAQDADEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKSPI 78 KL + + +A + A A A E L+ +GEY+ R ++C+ACHT GQP+AGG+E K P Sbjct: 3 KLISNVLTLASAALLAQAAYAQEDLLAKGEYLTRAANCVACHTVPGGQPFAGGVEFKLPF 62 Query: 79 GTIYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMY 138 G+++S NITPDP+ GIG +T ++F AL+ GI +DG YPA PY ++++S DDI A+ Sbjct: 63 GSLFSPNITPDPQTGIGAWTDDEFVSALQTGIGRDGKHYYPAFPYTSYSKMSRDDILAIK 122 Query: 139 AFFMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFVPSMTPGVDKSISDPEVARGEYLV 198 ++ ++PV + I +P + RW + W +F+ + P S E RG+YLV Sbjct: 123 G-YLDSLQPVEQAPRENHIGFPFNQRWGMVFWNLLFL-NDEPFQADSQRSAEWNRGKYLV 180 Query: 199 NGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSEDD 258 GPGHCGECH+PR V + + GN I W A ++ ++ G+G W D Sbjct: 181 EGPGHCGECHSPRNLFQAVSSERSLAGNL-------IQGWNAYNISADPVHGIGAWPTDV 233 Query: 259 IVTFLKSGRIDHSAVFGG-MADVVAYSTQHWSDDDLRATAKYLKSMPAVPEGKNLGQDDG 317 + +LK G + G MA+VV S +H +D D +A A +LK P EG Q Sbjct: 234 LAGYLKDGAAPGLGLSSGPMAEVVENSLRHLTDADRQAIAVFLKDSPPRSEGVPRPQQ-- 291 Query: 318 QTTALLNKGGQGNA-GAEVYLHNCAICHMNDGTGVNRMFPPLAGNPVVITDDPTSLANVV 376 L + G G+A G +++ CA CH DGTG L G V ++L ++ Sbjct: 292 ---VTLAEPGSGSALGNKLFAEACASCHRWDGTGNQSQTAMLLGLKTVNDPAASNLLGIL 348 Query: 377 AFGGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMRKGWGNNAPGTVSASDIQKLRT 435 G AP MP F N +DQE+A + +FM + +G + VS + K RT Sbjct: 349 LSG---HGAADAPVNRRMPSFGNIYTDQELAALSSFMLQRFGESG-AQVSVPAVAKRRT 403 Lambda K H 0.317 0.134 0.421 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: 628 Number of extensions: 42 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: 478 Length of database: 407 Length adjustment: 32 Effective length of query: 446 Effective length of database: 375 Effective search space: 167250 Effective search space used: 167250 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