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_015944627.1 DHAF_RS17500 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000021925.1:WP_015944627.1 Length = 448 Score = 479 bits (1232), Expect = e-139 Identities = 241/441 (54%), Positives = 315/441 (71%), Gaps = 1/441 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF KVL+ANRGEIA+R++RAC E+ + TVAV+SEAD+ HVR AD+A IGP + SY Sbjct: 1 MFKKVLIANRGEIALRIIRACREMDIETVAVFSEADRDALHVREADQAVCIGPHPSTKSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA DAIHPGYGFL+ENA FA E T++GPS A+E +G+K AR Sbjct: 61 LNIPNIISAAELTGVDAIHPGYGFLSENARFAEICESCGITFIGPSPRAIETMGDKATAR 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 M +A VPVVPG+ E E +A + GYPV IKA GGGG+G+++ + E+ Sbjct: 121 KTMIEAGVPVVPGSKEVLTDVESASVLAKEIGYPVMIKASAGGGGKGMRIAQNPKELAKS 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 + A+ E +A F N+ +Y+EKY+E PRHIE QILAD+HGNV HLGERDCSLQRR+QK++E Sbjct: 181 IQAAQSEAQAAFGNSEIYLEKYVEEPRHIEFQILADKHGNVIHLGERDCSLQRRNQKLLE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299 EAPS AL+ +LR+ +GEAA + +AA+Y++AGT+EFL++ G +YF+E+NTRIQVEH VT Sbjct: 241 EAPSSALTPELRKAMGEAAVKAAKAADYSSAGTIEFLLDKHGHYYFIEMNTRIQVEHPVT 300 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E VTG+D++K Q+RVAAGE L Q+DV+I G +ME RINAE EK F P+ GT+ Y P Sbjct: 301 EFVTGIDLLKAQIRVAAGEPLGIEQEDVQIRGWAMECRINAENSEKNFMPSPGTIEFYHP 360 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D A QG I YDSMI KLIV G+DREE + R +RAL EF IEG+ T IP Sbjct: 361 PGGPGVRVDSAAYQGYTIPPYYDSMIGKLIVWGADREEAIQRMKRALEEFYIEGVHTTIP 420 Query: 420 FHRLMLTDEAFREGSHTTKYL 440 FH +L + FR G T ++ Sbjct: 421 FHLKVLDNAFFRRGEVYTNFI 441 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: 653 Number of extensions: 24 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: 601 Length of database: 448 Length adjustment: 35 Effective length of query: 566 Effective length of database: 413 Effective search space: 233758 Effective search space used: 233758 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