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_043746657.1 AMB_RS13620 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_000009985.1:WP_043746657.1 Length = 447 Score = 471 bits (1211), Expect = e-137 Identities = 233/442 (52%), Positives = 311/442 (70%), Gaps = 1/442 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MF KVL+ANRGEIA+R+ RAC E+G+RTVAV+S AD HVR ADEA IGP A DSY Sbjct: 1 MFEKVLIANRGEIALRIHRACREMGIRTVAVHSTADNDAMHVRLADEAVCIGPPSARDSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +++ AA ADAIHPGYGFL+ENA+FA+ VE+ F ++GP+ D + +G+K A+ Sbjct: 61 LNKAAILSAASITGADAIHPGYGFLSENADFAQMVEEHGFVFIGPTPDHIRMMGDKITAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 ++DA +PVVPG+ D+ E VA GYPV IKA GGGG+G+KV + +E+ Sbjct: 121 QAVKDAGIPVVPGSDGSVDTEETALEVAASIGYPVLIKATAGGGGKGMKVARNAEELVES 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 ++ A+ E +A F NA VY+EKYL PRHIE+QILAD +G V HLGERDCSLQR+HQKV+E Sbjct: 181 WKLARNEAKAAFGNADVYMEKYLGKPRHIEMQILADNYGAVVHLGERDCSLQRKHQKVLE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EAPSPAL+ D R RIG+ A + Y NAGT+EFL E+GEFYF+E+NTR+QVEH +TE Sbjct: 241 EAPSPALNADQRARIGKIACDAIAKLGYRNAGTIEFLYENGEFYFIEMNTRLQVEHPITE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG+D+V+ Q+R+AAG L ++Q DV GH++E R+NAE P F P G + Y P Sbjct: 301 AITGIDLVREQIRIAAGAPLGYTQADVRFAGHALECRVNAEDP-VTFTPCPGRIEGYHAP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D + G I YDSMIAKLIV G+ R E L+R +RAL E+ IEG++T +P Sbjct: 360 GGLGVRVDSGLYAGYRIPPHYDSMIAKLIVFGNTRNEALMRLKRALGEYVIEGVKTTLPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDE 442 H ++ D F G + +L++ Sbjct: 420 HNRLVQDADFVNGDYDIHWLEK 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: 677 Number of extensions: 25 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: 447 Length adjustment: 35 Effective length of query: 566 Effective length of database: 412 Effective search space: 233192 Effective search space used: 233192 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 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