Align acyl CoA carboxylase carboxyltransferase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate WP_092348592.1 BLU87_RS11655 acetyl-CoA carboxylase carboxyltransferase subunit
Query= metacyc::MONOMER-13598 (524 letters) >NCBI__GCF_900107645.1:WP_092348592.1 Length = 574 Score = 288 bits (738), Expect = 3e-82 Identities = 179/522 (34%), Positives = 280/522 (53%), Gaps = 31/522 (5%) Query: 3 ITSEKSDMDKIIAQLREIKAKAFQGGGEDKIKAQHDKGKLTARERLALLFDEGSFNEIMP 62 I + ++++ + E+ + + +I+ QH K ++T ER+ +L D P Sbjct: 28 IAGKTGAYEEVMKEGYELTQRPIKSVAVGQIEKQHFKKRMTVWERIKVLTDND------P 81 Query: 63 LATTRATEFGLDKNKFYGDGVVTGWGKIEGRTVFAFSQDFTELGGTLGETHANKIGKVYE 122 + LD G +VTG I GR V + DFT G++ T+ K+ ++ Sbjct: 82 NILFQNWGKNLD-----GASLVTGILNIGGRDVALYGHDFTVRAGSIDATNGQKLARLMY 136 Query: 123 LALKVGAPVIGINDSGGARIQEGAIALEGYATVFKMNTLASGVIPQITIMAGPAAGGAVY 182 +A + G P+IG+NDS GA + G L+GYA F SGV+P + M G AGG Y Sbjct: 137 MAGEKGIPLIGMNDSAGAFVPAGVGGLDGYAEAFTALRKISGVVPTVMCMFGFNAGGGSY 196 Query: 183 SPALTDFIIMIKGDAYYMFVTGPEITKVVLGEEVTFQDLGGAVVHATKSGVVHFLAENEQ 242 P F+I + + + +TGP + K VLGE++T +DLGG VHA +GV +E Sbjct: 197 LPRQGSFVI--QPEETFFGLTGPGVVKSVLGEDITPEDLGGPKVHAA-TGVTDLTVADET 253 Query: 243 DAISIAKRLLSYLPSNNMEDPPYMDTGDPSDRETKDVESIV------PTDSAKPFDMREV 296 A+ A RL+SY+P NN P+++T DP DR+T ++ +++ PT PFD+ + Sbjct: 254 AALRTAVRLISYIPDNNHTMAPFLETSDPIDRKTWEINTLLKKAFNSPTGFNTPFDVSII 313 Query: 297 IYRIVDNGEFMEVHRHWAQNIVVGFARVAGNVIGIVANNSNTLGAAIDIDAADKAARFIR 356 I +I D+G++ E+ A+ + F R+ GNV+G VANNS ID D+A K ARF+R Sbjct: 314 IQQICDHGDYFEMQPTRAREAITAFGRLGGNVVGFVANNSAVSSGQIDCDSAVKIARFVR 373 Query: 357 FCDAFNIPLLSLVDTPGYIPGTEQEYKGIIRHGAKMLYAFSEATVPKISVIIRKSYGGAH 416 FC+ +NIPL+ + DT G++PG EQE +GI++ G ML + + P+I +I+R +YGGA+ Sbjct: 374 FCNIYNIPLIFMEDTTGFLPGREQEARGIVQAGRTMLDSIVDVRTPRILLILRNAYGGAY 433 Query: 417 IAMSIKNLGADLVYAWPTAEIAVTGPEGAVRILYKRDIQNSQNPDEFLKQKIAEYKKLFA 476 + + GADLV A PT +AV GP G +YK +++ + +KQ+IA A Sbjct: 434 ASYNNYPTGADLVLALPTTRLAVMGPAGK-EFVYKSELRKVRGA---VKQRIA------A 483 Query: 477 NPYWAAEKGLIDDVIEPKDTRRIIVNALSMLKNKREYRYPKK 518 N + G+ D + KD + L + + RY K+ Sbjct: 484 NILERTKAGM-DGLDAKKDAEKEAAEWLKLEEAALNQRYEKE 524 Lambda K H 0.318 0.137 0.394 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: 750 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 524 Length of database: 574 Length adjustment: 36 Effective length of query: 488 Effective length of database: 538 Effective search space: 262544 Effective search space used: 262544 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 (21.7 bits) S2: 53 (25.0 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