Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Echvi_3962 Echvi_3962 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Cola:Echvi_3962 Length = 499 Score = 481 bits (1238), Expect = e-140 Identities = 248/507 (48%), Positives = 336/507 (66%), Gaps = 20/507 (3%) Query: 3 KKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIV 62 +KIL+ANRGEIA R+++T R+MG+++VA+YS+ D+NA HV ADE+ +GP+P+++SY++ Sbjct: 5 RKILVANRGEIALRIMRTIREMGLKSVAVYSEVDKNAPHVLYADESYCLGPAPSHKSYLL 64 Query: 63 IDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKI 122 +++++A + GA+A+HPGYGFLSEN FA+ + G+ FIGP +IE MGDK+ +KK Sbjct: 65 GERIIEACQALGADAIHPGYGFLSENTAFAKKVADAGLIFIGPSPESIEIMGDKLAAKKA 124 Query: 123 AQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGFQ 182 ++ VPG I D EA K + EIGYP++IKASAGGGGKGMRI ++ E E + Sbjct: 125 VSHYDIPMVPGTDHAILDIQEAKKTAVEIGYPILIKASAGGGGKGMRIVQDEGEFEEQMK 184 Query: 183 SSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEEA 242 + +EA ++FGD +FIEK++T PRHIEIQ+LAD HGN ++L ERECS+QRR+QKV+EEA Sbjct: 185 RAVSEAQSAFGDGAVFIEKYITSPRHIEIQILADQHGNYLHLFERECSVQRRHQKVIEEA 244 Query: 243 PSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTEL 302 PS +++ RKAMG+ + +A+A Y AGTVEFIVD NFYFLEMNTRLQVEHPVTE+ Sbjct: 245 PSAVVNQEMRKAMGQAAIDVAKACQYYGAGTVEFIVDEALNFYFLEMNTRLQVEHPVTEM 304 Query: 303 ITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPV 362 ITG DLV + I +A G+ L QDD+T+ G AIE R+YAEDP NFLP IG+L YR Sbjct: 305 ITGKDLVREQIFIAEGQALSFAQDDLTILGHAIETRVYAEDPTNNFLPDIGKLATYR--- 361 Query: 363 EVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEA 422 P GP +R D G EG EI +YYDPMIAKL T+ DRP AI+ Sbjct: 362 ----------------LPQGP-GIRVDDGFREGMEIPIYYDPMIAKLVTFEEDRPKAIQK 404 Query: 423 MRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTRL 482 M A+D + + GI L F VM HP F GE T F+++ + + L Sbjct: 405 MVRAIDDYHITGISTTLSFARFVMLHPAFQSGEFDTKFVEKHFAPSKLAENFSEEEEEIL 464 Query: 483 AAAAAAMFRVAEIRRTRISGTLDNHER 509 A AA + A+ T ++G N+ + Sbjct: 465 ATIAAYLLPNAKQPSTNVNGQDQNNSK 491 Lambda K H 0.318 0.134 0.392 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: 840 Number of extensions: 38 Number of successful extensions: 2 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: 681 Length of database: 499 Length adjustment: 36 Effective length of query: 645 Effective length of database: 463 Effective search space: 298635 Effective search space used: 298635 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: 53 (25.0 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