Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_041936827.1 RL_RS28870 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000009265.1:WP_041936827.1 Length = 621 Score = 468 bits (1203), Expect = e-136 Identities = 279/668 (41%), Positives = 385/668 (57%), Gaps = 59/668 (8%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 M + +LIANRGEIA R+I++A+ +GI+T+AVYS+AD V ADEAI IGP PA +SY Sbjct: 1 MMESLLIANRGEIARRIIRSAKMLGIRTIAVYSEADAGLPFVREADEAIAIGPAPARESY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + +I+EA + SGA A+HPGYGFLSE DFA A+E AG++++G P AI AMG K +K Sbjct: 61 LSQTRILEAARKSGAAAIHPGYGFLSENADFAEAVEKAGIIWVGAPPAAIRAMGLKDAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 +L + +GV PGYMG + + IGYPV+IKA AGGGGKGMR + E Sbjct: 121 ELMQASGVPVTPGYMGADQSEERLAAEAENIGYPVLIKAVAGGGGKGMRRVDRPQDFAEL 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S + EAA +FGDDR+ IE+++ PRHIE+QV AD GNCV+L ER+CS+QRR+QKVIE Sbjct: 181 LASCRREAAAAFGDDRVLIERYIANPRHIEVQVFADMFGNCVHLFERDCSLQRRHQKVIE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDG-----QKNFYFLEMNTRLQV 295 EAP+P L+ ATR + + A A+AV Y AGTVEFI D + +F+EMNTRLQV Sbjct: 241 EAPAPGLEAATRAVICDAAVKAARAVNYVGAGTVEFIADASEGLREDRIWFMEMNTRLQV 300 Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355 EHPVTE ITG DLV ++VA+GE LP Q ++ +NGWA E+RLYAE+P +LPS GRL Sbjct: 301 EHPVTEAITGEDLVLWQLKVASGEPLPKMQDEIAMNGWAFEARLYAENPAAGYLPSTGRL 360 Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415 R P +R D+GV +G +I+ +YDPMIAK+ T P REAA+ ++ A Sbjct: 361 DHLRLP-------DTIRVDSGVDQGDDITAFYDPMIAKIVTHGPNREAALSKLAAACAGI 413 Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475 E+ + N + + P F I T F+ + + D V EP+ + +AA A+ Sbjct: 414 EIWPVKSNAGLLARIAVDPDFRAARIDTGFL-DRHDDRL---VATEPSESAIDSAATAL- 468 Query: 476 RVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSD 535 ++ D AL G + +S A D+ V G L Sbjct: 469 -----------------LKNTDSDPWTALTG--FRISGADDKR---VRIRIGDHLH---- 502 Query: 536 WTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPPD 595 W +P ++ + +G L A + P +E+ E Sbjct: 503 WGQSRP-----------ELEANTVAIGETTVLFDAGSAWPISLPVASEV-----EASQGA 546 Query: 596 TSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGAS 655 +L PMPGLV+ ++VA+GD V +G L TVEAMKME+ LRA G V+K+ + G Sbjct: 547 GDGAILSPMPGLVISVDVADGDRVAKGDRLLTVEAMKMEHSLRAPFDGIVEKLQVSSGIR 606 Query: 656 LRVDDVIM 663 + + +++ Sbjct: 607 VSENQLVV 614 Lambda K H 0.318 0.134 0.386 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: 1001 Number of extensions: 50 Number of successful extensions: 4 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: 666 Length of database: 621 Length adjustment: 38 Effective length of query: 628 Effective length of database: 583 Effective search space: 366124 Effective search space used: 366124 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: 54 (25.4 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