Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate 3609096 Dshi_2485 pyruvate carboxylase (RefSeq)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Dino:3609096 Length = 1145 Score = 374 bits (960), Expect = e-107 Identities = 203/450 (45%), Positives = 276/450 (61%), Gaps = 9/450 (2%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARA-ADSY 60 F K+L+ANRGEIA+RVMRA ELG +TVAVY+E DK H ADEAY IG +Y Sbjct: 4 FQKILIANRGEIAIRVMRAANELGKKTVAVYAEEDKLCLHRFKADEAYKIGEGLGPVAAY 63 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L + +I A+ + ADAIHPGYG L+EN +F + ++GP A+ M LG+K AR Sbjct: 64 LSIDEIIRVAKLSGADAIHPGYGLLSENPDFVDACVANGIAFIGPRAETMRALGDKASAR 123 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 + +A VPV+P T D + V+A A+ G+P+ +KA GGGGRG++ + DEV + Sbjct: 124 RVAIEAGVPVIPATEVLGDDMDKVRAEAEAIGFPLMLKASWGGGGRGMRPIFDPDEVADK 183 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 +RE EA F N Y+EK + RH+EVQIL D GN+ HL ERDCS+QRR+QKV+E Sbjct: 184 VREGRREAEAAFGNGEGYLEKMITRARHVEVQILGDSMGNIYHLWERDCSVQRRNQKVVE 243 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFL--VEDGEFYFMEVNTRIQVEHTV 298 AP+P LS RE++ E R+ Y AGTVEFL ++ GEF+F+EVN R+QVEHTV Sbjct: 244 RAPAPYLSSSQREQLCELGRKICAHVNYECAGTVEFLMDMDTGEFFFIEVNPRVQVEHTV 303 Query: 299 TEEVTGLDVVKWQLRVAAGEEL-----DFSQDDVEIEGHSMEFRINAEAPEKEFAPATGT 353 TEEVTG+D+V+ Q+ +A G+ L SQ DV++ GH+++ RI E P+ F P G Sbjct: 304 TEEVTGIDIVRAQILIAEGKSLVEATGMASQYDVQLNGHAIQCRITTEDPQNNFIPDYGR 363 Query: 354 LSTYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE 412 ++ Y G+GIR+D G I YDS++ K+ E + R +RAL EF I Sbjct: 364 ITAYRGATGMGIRLDGGTAYSGAVITRYYDSLLEKVTAWAPTPEAAIARMDRALREFRIR 423 Query: 413 GLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442 G+ T I F +L F +TTK++DE Sbjct: 424 GVSTNIAFVENLLKHPTFLNNQYTTKFIDE 453 Score = 50.8 bits (120), Expect = 3e-10 Identities = 43/136 (31%), Positives = 61/136 (44%), Gaps = 27/136 (19%) Query: 466 EEGEVTERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQ 525 E+GEV + F E+NG+ +V + R A AA+ A +P Sbjct: 1037 EDGEV--KVF-FELNGQPRQVRVPNRKA---------AASVAKRPKAEL----------- 1073 Query: 526 QVIEGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLV 585 G+ V A M G + +V V G V+ GD + +EAMKME + AER V V V Sbjct: 1074 ----GNPNHVGAPMPGVVASVAVQAGASVKEGDLLLTIEAMKMETGIHAERDAVVKAVHV 1129 Query: 586 GEGDSVDMGDVLLVLE 601 +D D+L+ LE Sbjct: 1130 TPAAQIDAKDLLVELE 1145 Lambda K H 0.312 0.132 0.371 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: 1444 Number of extensions: 60 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: 601 Length of database: 1145 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1103 Effective search space: 616577 Effective search space used: 616577 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 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