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 Synpcc7942_1379 Synpcc7942_1379 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__SynE:Synpcc7942_1379 Length = 453 Score = 456 bits (1174), Expect = e-133 Identities = 230/451 (50%), Positives = 313/451 (69%), Gaps = 1/451 (0%) Query: 2 FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYL 61 F+K+L+ANRGEIA+R++R CEELG+ T+AV+S D++ HV+ ADEA IG A ++ SYL Sbjct: 3 FNKILIANRGEIALRILRTCEELGIGTIAVHSTVDRNALHVQLADEAVCIGEAASSKSYL 62 Query: 62 DHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARS 121 + ++I AA +A AIHPGYGFLAENA FA D T++GPS D++ +G+K+ A+ Sbjct: 63 NIPNIIAAALTRNASAIHPGYGFLAENARFAEICADHHLTFIGPSPDSIRAMGDKSTAKE 122 Query: 122 LMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQF 181 MQ VP +PG+ + VA + GYPV IKA GGGGRG+++V +++ F Sbjct: 123 TMQRVGVPTIPGSDGLLTDVDSAAKVAAEIGYPVMIKATAGGGGRGMRLVREPADLEKLF 182 Query: 182 ETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEE 241 A+ E EA F N +Y+EK+++ PRH+E QILAD +GNV HLGERDCS+QRRHQK++EE Sbjct: 183 LAAQGEAEAAFGNPGLYLEKFIDRPRHVEFQILADAYGNVVHLGERDCSIQRRHQKLLEE 242 Query: 242 APSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVTE 300 APSPALS DLR+++G+AA + +A Y AGTVEFLV+ G FYFME+NTRIQVEH VTE Sbjct: 243 APSPALSADLRQKMGDAAVKVAQAIGYIGAGTVEFLVDATGNFYFMEMNTRIQVEHPVTE 302 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TGLD++ Q+R+A GE L F Q D+++ GH++E RINAE PE F P G ++ Y PP Sbjct: 303 MITGLDLIAEQIRIAQGEALRFRQADIQLRGHAIECRINAEDPEYNFRPNPGRITGYLPP 362 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG G+R+D V EI YDS+I KLIV G+ REE + R +RAL E I GL T + F Sbjct: 363 GGPGVRVDSHVYTDYEIPPYYDSLIGKLIVWGATREEAIARMQRALRECAITGLPTTLSF 422 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEA 451 H+LML F G T ++++V+ P +++ Sbjct: 423 HQLMLQMPEFLRGELYTNFVEQVMLPRILKS 453 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: 600 Number of extensions: 21 Number of successful extensions: 2 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: 453 Length adjustment: 35 Effective length of query: 566 Effective length of database: 418 Effective search space: 236588 Effective search space used: 236588 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 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