Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_007154498.1 MDG893_RS14185 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000170835.1:WP_007154498.1 Length = 667 Score = 481 bits (1237), Expect = e-140 Identities = 296/678 (43%), Positives = 400/678 (58%), Gaps = 36/678 (5%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACR+I+TA +MGI+ VAVYS+AD DA V MADEA IGPAAS ESY Sbjct: 1 MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSDADADARHVAMADEAFNIGPAASSESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 L ADKII K++GA+AVHPGYGFLSEN +F+ E I FIGP +IA MG K +K Sbjct: 61 LKADKIIEVAKESGAQAVHPGYGFLSENTQFAEACEANNIVFIGPPSSAIAAMGSKSAAK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 + A V +PGY+ P+ + A+K G+P+++KA AGGGGKG+RV + + Sbjct: 121 AIMETAGVPLVPGYHGDDQSPETLRKEAEKCGFPLLLKAVAGGGGKGMRVVERMEDFDDA 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 ++ E++N+FG+ + IE+Y+ +PRH+EIQV D G VYL ERDCS+QRRHQKV+E Sbjct: 181 LAAAKRESKNAFGNPDMLIERYLTQPRHVEIQVFCDKSGKGVYLAERDCSVQRRHQKVLE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAP+P + E RK+MGE AV A+A++Y AGTVEF+ F+F+EMNTRLQVEHPV Sbjct: 241 EAPAPGLSDETRKSMGEAAVKAAQAIDYVGAGTVEFLYD-VDGSFFFMEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE++TG DLVE ++VA+G+ LPL QA V+ G A+E RI AEDP + FLP+TG L Sbjct: 300 TEMVTGQDLVEWQLKVAWGDALPLEQAQVKTRGHALEARIYAEDPDQDFLPATGNLRYLS 359 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 P E VRVDTGV +G +IS++YD MIAKLIV +R+QAI RM AL + I G+ + Sbjct: 360 TPDE-SAHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAINRMVQALEHYRIAGVKT 418 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480 NI F AL F+ TGFI F S + D L+ A FV + ++ Sbjct: 419 NIRFLHALADAQPFREADLTTGFIEDHRELLFPKSRL--DTHKALVLAAGFVLEQ--RKS 474 Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIE-------GGYLVTYNGEKYELLSDW 533 +V P + W + N E A+P++ V ++Y++ Sbjct: 475 REVISTDPWSPFGRQNSWRM--NSE----YAQPLQLQVGEDIHELKVLERDDRYQVF--- 525 Query: 534 RQGQSLFNGTCNGEEFTLQ--VERHRMTYQLFHWGTRADMMVMSARAAELLALMP----- 586 G S++N T ++ LQ + HR++ H D +V+ ++ Sbjct: 526 -VGDSVYNLTAKLDDDYLQAVINGHRIS---VHGNLHNDQLVLFYEGDTFQCILYRETYG 581 Query: 587 -EKAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKI 645 E+ A + S L +PM G + V VG V AG+ L ++EAMKME+ +KA D V I Sbjct: 582 FEEMAGEGS--LAAPMNGAIVAVQTKVGDTVTAGQSLVIMEAMKMEHAIKAPADGVVTDI 639 Query: 646 SVTAGSSLSVDEIIIEFE 663 G +S +I E Sbjct: 640 FFAEGDQVSEGAELIAIE 657 Lambda K H 0.319 0.135 0.391 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: 1068 Number of extensions: 41 Number of successful extensions: 5 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: 663 Length of database: 667 Length adjustment: 38 Effective length of query: 625 Effective length of database: 629 Effective search space: 393125 Effective search space used: 393125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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