Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate AZOBR_RS21105 AZOBR_RS21105 acetyl-CoA carboxylase
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__azobra:AZOBR_RS21105 Length = 666 Score = 828 bits (2139), Expect = 0.0 Identities = 429/667 (64%), Positives = 517/667 (77%), Gaps = 7/667 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 +F KILIANRGEIACRVI+TAR++GIKTVAVYS+AD++AL VEMADEAV IG A S +SY Sbjct: 1 LFSKILIANRGEIACRVIRTARRLGIKTVAVYSDADRNALHVEMADEAVHIGAAPSAQSY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 L+ D+I+ ACK+TGA+AVHPGYGFLSE EF L GI FIGP ++I MGDKIESK Sbjct: 61 LLIDRIVDACKKTGAQAVHPGYGFLSEKREFQEALAAAGIAFIGPDAHAIQAMGDKIESK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KLA A V+T+PGY I AV IA+ IGYPVMIKASAGGGGKG+RVA+ND EA EG Sbjct: 121 KLAKAAGVSTVPGYLGVIADDSEAVTIARDIGYPVMIKASAGGGGKGMRVAWNDEEAREG 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 F S NEAR+SF DDRVF+EKY+ +PRHIEIQVL D G +YL ER+CSIQRRHQKVIE Sbjct: 181 FRSAQNEARSSFADDRVFVEKYIQQPRHIEIQVLADGQGTALYLGERECSIQRRHQKVIE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAPSPF+D RKAMGEQAVALARAV+Y+SAGTVEF+V A + FYFLEMNTRLQVEHPV Sbjct: 241 EAPSPFLDAATRKAMGEQAVALARAVDYKSAGTVEFIVD-AERNFYFLEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TEL+TGLDLVE MIRVA GEKL L Q D+ ++GWA+E R+ AEDPFR FLPSTGRL ++ Sbjct: 300 TELVTGLDLVELMIRVAAGEKLTLKQEDIHLHGWAIESRVYAEDPFRNFLPSTGRLTHYR 359 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PP+E D VRVDTGVY+GGEISMYYD MIAKL G++R+ AIARMR+AL+ + IRG+S Sbjct: 360 PPSE-DPHVRVDTGVYEGGEISMYYDPMIAKLCSWGSTRDAAIARMREALDQYYIRGVSH 418 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480 NIPF A+LM + RF G T FIA+EYP GF AS +P ++PA+LI VAA +HR DR Sbjct: 419 NIPFLASLMANQRFVEGRLTTNFIAEEYPTGFHASDLPPEEPAVLIAVAAVIHRCLNDRD 478 Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEG-----GYLVTYNGEKYELLSDWRQ 535 Q+SG++PG++ +V D+WVV+ +G +HPV +P +G GY V + G + + SDW Sbjct: 479 IQISGKMPGNKVRVRDDWVVVMDGTQHPVHVRPTDGSPQRIGYTVDFEGRHHVVWSDWTL 538 Query: 536 GQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSK 595 GQ LF GT NG +QV+R + Y+L H G++A + V++ AA L ALMP KA PD+SK Sbjct: 539 GQPLFRGTVNGAHVCVQVDRVGVGYRLSHSGSQALVKVLTPNAARLDALMPVKAPPDMSK 598 Query: 596 FLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSV 655 FLLSPMPGLL V+V GQEVKAGE LAV+EAMKMENIL+A QD V K+ T GSSL+V Sbjct: 599 FLLSPMPGLLVSVAVTEGQEVKAGEVLAVVEAMKMENILRAAQDGTVSKVHATPGSSLAV 658 Query: 656 DEIIIEF 662 D+ I+EF Sbjct: 659 DQKILEF 665 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: 1170 Number of extensions: 46 Number of successful extensions: 4 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: 666 Length adjustment: 38 Effective length of query: 625 Effective length of database: 628 Effective search space: 392500 Effective search space used: 392500 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 Apr 09 2024. 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