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 WP_028314054.1 G491_RS0106895 carbamoyl phosphate synthase large subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000429905.1:WP_028314054.1 Length = 1107 Score = 332 bits (851), Expect = 5e-95 Identities = 189/454 (41%), Positives = 280/454 (61%), Gaps = 18/454 (3%) Query: 4 KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63 K+L ANRGEIAVR+ RA EL + TVAVYS+ D H+R ADEA + R A +YL+ Sbjct: 4 KILAANRGEIAVRIFRAANELNIPTVAVYSQDDGASLHIRMADEAIALN-GRGAAAYLNM 62 Query: 64 ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123 ++++ AA+K AIHPGYGFL+EN EFA K ++ ++GPS + + G+KT+AR L Sbjct: 63 DAILTAAQKTGCTAIHPGYGFLSENPEFAAKCAEAGLVFIGPSPENLRLFGDKTQARLLA 122 Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYP--VAIKAEGGGGGRGLKVVHSEDEVDGQF 181 ++ VP++PGT S ++V++ + G V IKA GGGGRG++ V+ ++ + Sbjct: 123 KECGVPLLPGTMG-GTSLDEVRSFMNGLGKDGAVMIKAVSGGGGRGMRPVYDSAGLEEAY 181 Query: 182 ETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEE 241 + E +A F +YVE+ + RHIE+Q++ D G V H ER+CSLQRR+QKV+E Sbjct: 182 SICRSEAQAAFGAGDLYVERLIPRARHIEIQVIGDGTGAVSHFWERECSLQRRNQKVVEF 241 Query: 242 APSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV------EDGEFYFMEVNTRIQVE 295 APSPAL+++LR + AA + + + T EFLV ++G F+FMEVN R+QVE Sbjct: 242 APSPALTQELRGLLVNAALKMAEKVKLKSLATFEFLVDADAETQEGSFFFMEVNPRLQVE 301 Query: 296 HTVTEEVTGLDVVKWQLRVAAGE---ELDFSQDDVEIE-GHSMEFRINAEA--PEKEFAP 349 HTVTEEVTG+D+V+ Q+R+AAG+ +L Q DV G++++ RINAE E P Sbjct: 302 HTVTEEVTGVDLVQAQIRIAAGQTLADLGLEQKDVPAPLGYALQCRINAETILENGEVRP 361 Query: 350 ATGTLSTYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDR--EEVLVRAERALN 407 + G L ++ PP G G+R+D A G EI ++DS++AKL V R + +A RAL Sbjct: 362 SGGRLESFCPPTGPGVRVDAAGYPGYEINPNFDSLLAKLTVHSRSRSFSDATAKAYRALC 421 Query: 408 EFDIEGLRTVIPFHRLMLTDEAFREGSHTTKYLD 441 EF I+G+ +P + +L +T++++ Sbjct: 422 EFRIDGVAANVPLLQNLLIHPDVTSNQISTRFIE 455 Score = 45.4 bits (106), Expect = 1e-08 Identities = 27/69 (39%), Positives = 38/69 (55%) Query: 533 ESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVD 592 E V A MQGT++ E EGD V G V ILEAMKM++ + A G V + G+++ Sbjct: 500 EPVEAPMQGTVVQFEAAEGDMVCEGQAVAILEAMKMQHLIKAPVSGLVRWICSEPGETLA 559 Query: 593 MGDVLLVLE 601 L+ +E Sbjct: 560 ECQPLMFVE 568 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: 1392 Number of extensions: 65 Number of successful extensions: 8 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: 1107 Length adjustment: 41 Effective length of query: 560 Effective length of database: 1066 Effective search space: 596960 Effective search space used: 596960 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 24 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