Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_101590190.1 BJEO58_RS14660 ATP-grasp domain-containing protein
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_900169175.1:WP_101590190.1 Length = 454 Score = 408 bits (1048), Expect = e-118 Identities = 208/447 (46%), Positives = 298/447 (66%), Gaps = 4/447 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 + ++LVANRGEIA R+ R C+ LG+ TVAVYS+AD++ HVR AD IG A A+ SY Sbjct: 4 VIKRILVANRGEIACRIFRTCDLLGIETVAVYSDADENSKHVRMADRTVRIGEALASSSY 63 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 LD E+V+ AA + DAIHPGYGFL+EN+EFARK+++ TWVGP ++M+ + EK AR Sbjct: 64 LDIEAVLRAASDSGVDAIHPGYGFLSENSEFARKIQELGLTWVGPDPESMDSMSEKVPAR 123 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 +LM +A VPVVPGT+ D+ + A + GYP+ +KA GGGG G+ VV S+ E++ Sbjct: 124 ALMLEAGVPVVPGTSGSVDTLDHALLSAQEIGYPMVLKATAGGGGLGMSVVTSDAELEKS 183 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 ++ +R+ E F N SVY+EKY+E+ +HIEVQ+L V +G+R+CS+QRRHQKV+E Sbjct: 184 YDATRRKAERAFGNGSVYLEKYIESAKHIEVQVLGLNSDKVAVIGDRECSVQRRHQKVLE 243 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE--DGEFYFMEVNTRIQVEHTV 298 EAP+P LSE R+ + A++ +Y AGTVEF+ + EFYF+E+NTR+QVEH V Sbjct: 244 EAPAPTLSESERDWLYVMAQKVAEKVKYRGAGTVEFIFDRMTREFYFLEMNTRLQVEHPV 303 Query: 299 TEEVTGLDVVKWQLRVAAGEELDFSQ-DDVEIEGHSMEFRINAEAPEKEFAPATGTLSTY 357 TE VTGLD+V+ Q+ +AAG+ELD ++ D +GH++EFR+ AE P + F P G ++T+ Sbjct: 304 TELVTGLDLVELQIHIAAGQELDLARLDRPTPQGHAIEFRVYAEDPVR-FLPGPGEITTW 362 Query: 358 DPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTV 417 P G G+R+D GD + YD ++AKL V DR+ VL A EFD+ G +T Sbjct: 363 AEPSGPGVRVDSGYDVGDIVTPYYDPLLAKLCVHDVDRDHVLHALGEAAQEFDVSGPKTN 422 Query: 418 IPFHRLMLTDEAFREGSHTTKYLDEVL 444 + ++ D +F +G + T+ L V+ Sbjct: 423 LALVEGIVGDPSFVDGEYDTEMLTRVV 449 Lambda K H 0.312 0.132 0.371 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: 666 Number of extensions: 31 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: 601 Length of database: 454 Length adjustment: 35 Effective length of query: 566 Effective length of database: 419 Effective search space: 237154 Effective search space used: 237154 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 52 (24.6 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