Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_026606601.1 METAC_RS0107890 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000427445.1:WP_026606601.1 Length = 668 Score = 722 bits (1863), Expect = 0.0 Identities = 387/671 (57%), Positives = 472/671 (70%), Gaps = 10/671 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MFKK+LIANRGEIACRVI+TAR+MGI TVAVYS+AD++A HV++ADEA+ IGP PA SY Sbjct: 1 MFKKLLIANRGEIACRVIRTARRMGIATVAVYSEADKHAQHVALADEALPIGPAPAAHSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + I+KI+EA K SGAEAVHPGYGFLSER DFA AL GV F+GP AIEAMGDKI SK Sbjct: 61 LAIEKILEACKQSGAEAVHPGYGFLSERADFAQALCDMGVAFVGPHPRAIEAMGDKIASK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 KLA+ A VSTVPG++G I D A I+ EIGYPVMIKASAGGGGKGMRIA S E+ + Sbjct: 121 KLARAANVSTVPGFVGAIEDEAHARAIAEEIGYPVMIKASAGGGGKGMRIAHSGDEITDC 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 + +EA SFGD+R+ IEKF+ PRHIEIQVL DK+G ++L ERECSIQRR+QKV+E Sbjct: 181 LARAASEAKASFGDERLLIEKFIADPRHIEIQVLGDKYGGLIHLGERECSIQRRHQKVVE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSPF+DEA R+ MGEQA ALA AV Y SAGTVEF+V K+FYFLEMNTRLQVEHPVT Sbjct: 241 EAPSPFVDEAMRREMGEQAIALAAAVNYDSAGTVEFVVAQDKSFYFLEMNTRLQVEHPVT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 EL+TG+DLVE+MI+VAAG L Q D+ + G A+ESR+YAEDP RNFLPS+GRLT YRP Sbjct: 301 ELVTGVDLVEEMIKVAAGAPLSISQRDVHLRGAAIESRIYAEDPARNFLPSVGRLTTYRP 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P + +R D GV EG EIS++YDPM+AKL T A R AAI+ ALD F +EG+ Sbjct: 361 PAQGHEDGITLRLDGGVLEGDEISIHYDPMVAKLVTHAGDRAAAIDAQARALDQFAIEGV 420 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480 GHN+PF+ A+M HPRF GD++TAFIA EYP GF + AAAM+ + Sbjct: 421 GHNIPFLAALMAHPRFKAGDLSTAFIAREYPGGFAPLAPEGEAAHLFVVVAAAMDHLLNE 480 Query: 481 RRTRISGTMN-----NHERHVGVDWVVALQGESYHVSIAADREGSTVSF-SDGSSLRVTS 534 R+ ISG M ER D V L + V + +G + F + G + S Sbjct: 481 RKRLISGQMRASVPVAFER----DRSVILGKTRHDVKLEEADDGLQIRFEATGHLHQCAS 536 Query: 535 DWTPGQPLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPEKLPP 594 DW PG+P+ + +VDG + ++ + G+ L + V T R+AELA LMP+K P Sbjct: 537 DWAPGRPIWTGVVDGEEVGFRIRSLLNGWSLAHGPYAAQAYVYTRREAELAALMPDKRPA 596 Query: 595 DTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKIAAAPGA 654 D +K LLCPMPGL+ INV+ G +V+ G+ L VEAMKMEN L+A + GTVKKI A G Sbjct: 597 DRTKLLLCPMPGLIKAINVSAGQQVKAGETLCVVEAMKMENALQAAQDGTVKKIFAREGE 656 Query: 655 SLRVDDVIMEF 665 SL VD IMEF Sbjct: 657 SLAVDAAIMEF 667 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: 1164 Number of extensions: 48 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: 666 Length of database: 668 Length adjustment: 38 Effective length of query: 628 Effective length of database: 630 Effective search space: 395640 Effective search space used: 395640 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