Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS25130 RR42_RS25130 pyruvate carboxylase
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Cup4G11:RR42_RS25130 Length = 1167 Score = 382 bits (981), Expect = e-110 Identities = 205/481 (42%), Positives = 290/481 (60%), Gaps = 42/481 (8%) Query: 3 KKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPAN-QSYI 61 K +LIANR EIA RV++ A +M I+TVAIYS DR ALH ADE+ +G +Y+ Sbjct: 7 KSLLIANRSEIAIRVMRAAAEMNIRTVAIYSKEDRLALHRFKADESYLVGEGKKPLAAYL 66 Query: 62 VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121 ID ++ RQ +A+HPGYGFLSEN FA+A+ G+ +IGP + +G+K+ ++ Sbjct: 67 DIDDILRIARQAKVDAIHPGYGFLSENPDFAQAVMDAGIRWIGPSPEVMRKLGNKVAARN 126 Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGF 181 A EA V +P L D DE +++ IGYP+M+KAS GGGG+GMR+ N+ + Sbjct: 127 AAIEAGVPVMPATDPLPRDLDECKRLAAGIGYPLMLKASWGGGGRGMRMLENEQDLETAL 186 Query: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEE 241 +++ EA ++FG+D +++EK V RH+E+Q L D HGN ++L ER+C++QRRNQKVVE Sbjct: 187 PAARREALSAFGNDEVYVEKLVRNARHVEVQALGDAHGNLVHLYERDCTVQRRNQKVVER 246 Query: 242 APSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR-NFYFLEMNTRLQVEHPVT 300 AP+P+LD+A R A+ + + L +AVGY AGT+EF++D D FYF+E+N R+QVEH VT Sbjct: 247 APAPYLDDAGRAALCDAAMRLMRAVGYTHAGTIEFLMDADSGQFYFIEVNPRIQVEHTVT 306 Query: 301 ELITGVDLVEQMIRVAAGEKLPMT-------------------QDDVTLTGWAIENRLYA 341 EL+TGVD+V+ IR+ G + MT Q ++L G A++ R+ Sbjct: 307 ELVTGVDIVKAQIRITEGGHIGMTENTRDADGKIVVRAAGVPEQAGISLNGHALQCRITT 366 Query: 342 EDPYRNFLPSIGRLTRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTG-VYEGGEISM 400 EDP FLP GRL+ YR AAG VR D G Y G I+ Sbjct: 367 EDPENGFLPDYGRLSAYRS----AAG----------------FGVRLDAGTAYGGAVITP 406 Query: 401 YYDPMIAKLCTWGPDRPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAF 460 YYD ++ K+ TW P P +I M AL F + G+ NL F+ V++HP F G++TT F Sbjct: 407 YYDSLLVKVTTWAPTAPESIRRMDRALREFRIRGVASNLQFLENVINHPAFRSGDVTTRF 466 Query: 461 I 461 I Sbjct: 467 I 467 Score = 50.4 bits (119), Expect = 5e-10 Identities = 23/71 (32%), Positives = 38/71 (53%) Query: 609 PDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATVTKINAGAG 668 P + PMPG +V + V+ G V G L +EAMKME + A++ + ++ G Sbjct: 1094 PGNPLHVAAPMPGAIVTVAVQPGQRVAAGTTLLALEAMKMETHIAADRDCEIAAVHVQQG 1153 Query: 669 DSLAVDDVIME 679 D +A D+++E Sbjct: 1154 DRVAAKDLLIE 1164 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: 1839 Number of extensions: 84 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 1167 Length adjustment: 43 Effective length of query: 638 Effective length of database: 1124 Effective search space: 717112 Effective search space used: 717112 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: 56 (26.2 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