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 8499651 DvMF_0417 pyruvate carboxylase (RefSeq)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Miya:8499651 Length = 1234 Score = 317 bits (813), Expect = 1e-90 Identities = 199/518 (38%), Positives = 288/518 (55%), Gaps = 15/518 (2%) Query: 5 VLVANRGEIAVRVMRACEE-LGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63 +LVANRG A R+ R+ E V ++ DK A E +G A YLD Sbjct: 18 ILVANRGIPARRICRSIRERFDAVAVMTATDIDKTSPAASAAQELLLLGSDPRA--YLDI 75 Query: 64 ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123 + +I A++ AIHPG+GF +E+ F K + + T++G +A+AM LG K + R L Sbjct: 76 DHIIALAKQRGIVAIHPGWGFASEDERFPAKCKAAGLTFIGSTAEAMNLLGNKVQVRKLA 135 Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183 + D+PVVPG+ E A + + D+ G PV +KAEGGGGGRG+ +H +E+ F Sbjct: 136 KKLDIPVVPGS-EGAVDIPTARTIIDEIGLPVMLKAEGGGGGRGIFAIHRAEELSDAFMK 194 Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243 A +A F N +YVEKYL + RHIE+Q++AD +GNV ERDC++QR HQK+IE P Sbjct: 195 ASTMAQASFGNPRLYVEKYLPSVRHIEIQVIADMYGNVFAFDERDCTVQRNHQKLIEITP 254 Query: 244 SP--ALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVTE 300 SP ++ +LRER+ E +R VR Y + TVEFLV DG Y +EVNTR+QVEH +TE Sbjct: 255 SPWSGITPELRERLKEYSRMLVREVGYHSLCTVEFLVTADGTPYLIEVNTRLQVEHGITE 314 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 G+D+V+ Q+ VA G L F++++ + +M+ RIN E P+ FAP +G +S Y P Sbjct: 315 CRYGIDLVEEQIAVAFGARLRFTEENTTPQHVAMQVRINCEDPQNHFAPNSGLVSRYVSP 374 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG G+R+D + G E +YDS + LI G E+VL ER L E+ I G++T +PF Sbjct: 375 GGPGVRLDSNMCAGYEFPSNYDSAGSLLIAYGQGWEKVLGIMERCLGEYVIGGIKTTVPF 434 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVTERTFTVEVN 480 ++ +L FR G T ++ PE + +PEA EV+ + + V Sbjct: 435 YKQVLKHPKFRAGDLDTNFIANT--PELM--CYSDLAPEAERLARLVAEVSAKGYNPYVQ 490 Query: 481 GKRF---EVSLEERGAPAIP-LGGASAAASASKPSGPR 514 + E R P +P + G A + P+G R Sbjct: 491 LGEYRTRETPRMPRFEPVLPHIPGTVRRAPSPYPTGDR 528 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: 1465 Number of extensions: 74 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: 601 Length of database: 1234 Length adjustment: 42 Effective length of query: 559 Effective length of database: 1192 Effective search space: 666328 Effective search space used: 666328 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