Align propionyl-CoA carboxylase (EC 6.4.1.3) (characterized)
to candidate CCNA_03320 CCNA_03320 biotin carboxylase
Query= BRENDA::Q9X4K7 (530 letters) >FitnessBrowser__Caulo:CCNA_03320 Length = 1078 Score = 241 bits (614), Expect = 1e-67 Identities = 172/530 (32%), Positives = 256/530 (48%), Gaps = 47/530 (8%) Query: 5 EEQQPDIHTTAGKLADLRRRIEEATHAGSARAVEKQHAKGKLTARERIDLLLDEGSFVEL 64 E + D+ LA++ R AV K+ G TARE ID L+D GSF+E Sbjct: 555 ETVEQDLDALRPDLAEVVARHRHTLDEARPEAVAKRRKTGHRTARENIDDLVDPGSFLEY 614 Query: 65 DEFA-----RHRSTNFGLDANRPYGDGVVTGYGTVDGR-------PVAVFSQDFTVFGGA 112 A R RST L AN P DG++TG GTV+G A + DFTV G Sbjct: 615 GALAIAAQKRRRSTE-DLIANTP-ADGLITGIGTVNGALFPPDKARTAALAYDFTVLAGT 672 Query: 113 LGEVYGQKIVKVMDFALKTGCPVVGINDSGGARI--QEGVASLGAYGEIFRRNTHASGVI 170 G + +K ++M PVV + GG R + A G FR SG++ Sbjct: 673 QGAMNHRKSDRLMALIADQKLPVVWFAEGGGGRPGDTDTTAVAGLDVPTFRSFAQLSGLV 732 Query: 171 PQISLVVGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVGF---EELGGA 227 P+I++V G C G +++ ++ + S++ + GP +I+ G +G EE+G + Sbjct: 733 PKIAIVAGRCFAGNAAIAGLSEI-IIATRDSNLGMGGPAMIE---GGGLGVFRPEEIGPS 788 Query: 228 RTHNSTSGVAHHMAGDEKDAVEYVKQLLSYLPSNNLSEPPAFPEEADLAVTDEDAELDTI 287 H +GV +A DE A KQ LSY F + L Sbjct: 789 -AHQWKNGVIDILADDEAHATRLAKQALSY-----------FQGTLSTWTAPDQRRLRHA 836 Query: 288 VPDSANQPYDMHSVIEHVLDDAEFFETQPLFAPNILTGFGRVEGRPVGIVANQPMQFAGC 347 +P++ + YD+ +I H++D+ F E + FA ++TG R+EGRP+G++AN P G Sbjct: 837 IPENRLRVYDVRGLINHLVDEGSFLELRGGFAAGMVTGLIRIEGRPMGLIANDPRHLGGA 896 Query: 348 LDITASEKAARFVRTCDAFNVPVLTFVDVPGFLPGVDQEHDGIIRRGAKLIFAYAEATVP 407 +D +EKAARF++ CDAF +PVL+ D PGF+ G D E +RR ++ A A+ P Sbjct: 897 IDCEGAEKAARFLQLCDAFALPVLSLCDTPGFMVGPDSEDAAAVRRVSRQFIAGAKLRSP 956 Query: 408 LITVITRKAFG-GAYDVMGSKHLGADLNLAWPTAQIAVMGAQGAVNILHRRTIADAGDDA 466 L T++TRK +G GA + G AWPT + MG +GAV + +R+ + +A Sbjct: 957 LFTIVTRKGYGLGAQAMAGGSFHSPAFIAAWPTGEFGGMGLEGAVKLGYRKEL-----EA 1011 Query: 467 EATRARLIQEYEDALLNPYTA------AERGYVDAVIMPSDTRRHIVRGL 510 E + Y+ + Y A A +DAVI P+DTRR ++ GL Sbjct: 1012 ETDPVKQKALYDQLVARLYAAGKATSMAAALEIDAVIDPADTRRWVIGGL 1061 Lambda K H 0.318 0.136 0.398 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: 1378 Number of extensions: 78 Number of successful extensions: 9 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: 530 Length of database: 1078 Length adjustment: 40 Effective length of query: 490 Effective length of database: 1038 Effective search space: 508620 Effective search space used: 508620 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: 55 (25.8 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