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 6939098 Sama_3196 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__SB2B:6939098 Length = 454 Score = 375 bits (964), Expect = e-108 Identities = 202/446 (45%), Positives = 276/446 (61%), Gaps = 6/446 (1%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61 F +VLVANRGEIAVR++RAC +LG+ TVA+YS ADK H A IGPA A DSYL Sbjct: 7 FKRVLVANRGEIAVRIIRACHQLGLETVAIYSSADKGALHTLLATHCLCIGPAAAKDSYL 66 Query: 62 DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121 + +++EAA+ ADAIHPGYGFLAE A FAR V ++ ++GP AD + +G+K A Sbjct: 67 NINAILEAAKLTAADAIHPGYGFLAERAGFARAVTEAGLVFLGPDADTIATMGDKVSAIK 126 Query: 122 LMQDADVPVVPGTTEPA-DSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 ++ +P +PG+ D V+A+A D GYPV IKA GGGGRG++ V S DE+ Sbjct: 127 SIKAVGIPTLPGSDGALNDDMNAVEALATDIGYPVLIKASAGGGGRGMRRVDSADELASA 186 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + E A F + +VY+EK+L PRHIE Q+LAD + LGERDCS QRRHQK+IE Sbjct: 187 IALTRSEALAAFGDNTVYLEKFLTHPRHIEFQMLADGEAAL-CLGERDCSAQRRHQKLIE 245 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EAP+ ++ + + + R Y GT EFL +DG F+F+E+NTRIQVEHTVTE Sbjct: 246 EAPALGIAREKIREMADICEAACRRLGYRGVGTFEFLYQDGAFFFIEMNTRIQVEHTVTE 305 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 VTGLD++ WQL+VA G L +++GH++E RINAEAP+ + P+ G ++ P Sbjct: 306 MVTGLDLIAWQLKVALGHPL---PPRPQVQGHAIECRINAEAPQSQL-PSPGVITQLRVP 361 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG G+R D + G + YDS+I KLI G REE R +AL E +I+G+ Sbjct: 362 GGPGVRWDSYLFPGAMVPAFYDSLIGKLICHGVTREEATARLRQALTELEIQGIAINKSL 421 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDP 446 H ++ +AF+ ++D + P Sbjct: 422 HLQLIACDAFQPWQRDIHFVDALSAP 447 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: 567 Number of extensions: 24 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: 454 Length adjustment: 35 Effective length of query: 566 Effective length of database: 419 Effective search space: 237154 Effective search space used: 237154 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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