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 SMc01345 SMc01345 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Smeli:SMc01345 Length = 449 Score = 424 bits (1091), Expect = e-123 Identities = 210/444 (47%), Positives = 301/444 (67%), Gaps = 2/444 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 M SK+L+ANRGEIA+RV+RAC+ELG+ TVAV+S AD HVR ADE+ IGP + +SY Sbjct: 3 MISKILIANRGEIALRVLRACKELGIATVAVHSTADSDAMHVRLADESVCIGPPPSRESY 62 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++ A ADA+HPGYGFL+ENA+FA ++ T++GP+A+ + +G+K A+ Sbjct: 63 LNIHQIVAACEITGADAVHPGYGFLSENAKFADILDAHGITFIGPTAEHIRLMGDKITAK 122 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 ++ +PVVPG+ E+ +A G+PV IKA GGGGRG+KV +E+E++ Sbjct: 123 KTAEELGIPVVPGSDGEV-RPENALEIARQIGFPVLIKATAGGGGRGMKVARTEEELENA 181 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 TA+ E A F N +VY+EK+L PRHIE+Q++ D GN HLGERDCSLQRRHQKV E Sbjct: 182 VATARSEAAAAFGNDAVYMEKFLGKPRHIEIQVVGDGEGNAIHLGERDCSLQRRHQKVWE 241 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EA SPAL+ + R +IG+ ++ +Y AGT+EFL E+GEFYF+E+NTR+QVEH +TE Sbjct: 242 EANSPALNVEQRMKIGQVCADAMKKLKYRGAGTIEFLYENGEFYFIEMNTRLQVEHPITE 301 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 +TG+D+V Q+RVA+G L Q+D+ GH++E RINAE P + F P+ GT++ + P Sbjct: 302 AITGIDLVHEQIRVASGAGLSAKQEDIVFSGHAIECRINAEDP-RTFVPSPGTITHFHAP 360 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+R+D QG I YDS+I KLIV G R E ++R R L+EF I+G++T +P Sbjct: 361 GGLGVRVDSGAYQGYRIPPYYDSLIGKLIVHGRTRVECMMRLRRVLDEFVIDGIKTTLPL 420 Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444 + ++ ++ G + +L+ L Sbjct: 421 FQDLINNQDIANGDYDIHWLEHHL 444 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: 655 Number of extensions: 30 Number of successful extensions: 3 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: 449 Length adjustment: 35 Effective length of query: 566 Effective length of database: 414 Effective search space: 234324 Effective search space used: 234324 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