Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate 207299 DVU1834 pyruvate carboxylase, putative
Query= metacyc::MONOMER-13597 (509 letters) >MicrobesOnline__882:207299 Length = 1234 Score = 316 bits (810), Expect = 3e-90 Identities = 193/474 (40%), Positives = 279/474 (58%), Gaps = 12/474 (2%) Query: 7 VLVANRGEIATRVLKAIKE-MGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 +LVANRG A R+ ++I+E A+ ++ DK + A E +G P +YL+I Sbjct: 18 ILVANRGIPARRICRSIRERFDAVAVMTATDVDKTSPAASAAQELLLLGADPR--AYLDI 75 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 + II A++ V AIHPG+GF SE+ F +AG+TFIG ++E M + +K+ ++LA Sbjct: 76 DRIISLAKQRGVVAIHPGWGFASEDDRFPSKCHEAGLTFIGSTAEAMNLLGNKVQVRKLA 135 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 GVP PGS+G V I A KL ++IG PIM+KA GGGG GI + ++ +L D + + Sbjct: 136 RKLGVPVVPGSEGAV-DIPTARKLIDEIGLPIMLKAEGGGGGRGIFAIRDESELDDAFFK 194 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 +A +FG LF+EKY + RHIE Q+I D YGN ER+C+IQR +QKLIE P Sbjct: 195 ASTMAQASFGNPRLFVEKYLESVRHIEIQVIADMYGNAFAFDERDCSIQRNHQKLIEITP 254 Query: 246 S--PALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 S P + E RE + E + + Y +L T E + S + Y +E+N RLQVEH T Sbjct: 255 SPWPGITPELREKLKEYSKMLVREVGYHSLATVEFLVT-ASGEAYLIEVNTRLQVEHGIT 313 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E + IDLV+ QI +A G L ++E N + A++ RIN ED F+ +SG V+ Y Sbjct: 314 ECRYGIDLVEEQIAVAFGAQLRLTEE--NTKPVHHAMQVRINCEDPQAGFSPNSGLVSRY 371 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P GPGVR+DS + +G PP YDS S LI YG+ + + R L++Y IGG+KTT Sbjct: 372 VSPGGPGVRLDSNMCAGYEFPPNYDSAGSLLITYGQGWQKVLGIMERCLSEYIIGGLKTT 431 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQKTDQFVKY--LREQEEIKAAIAAEIQSRG 475 I YK +M+ P F+ G F T++I++ T + + Y L + E A + AEI ++G Sbjct: 432 IPFYKQVMKHPRFRAGDFDTNFIAE-TPELMCYTDLAPEGERLARLVAEISAKG 484 Lambda K H 0.317 0.135 0.385 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: 1293 Number of extensions: 43 Number of successful extensions: 5 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: 509 Length of database: 1234 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1193 Effective search space: 558324 Effective search space used: 558324 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: 55 (25.8 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