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 N515DRAFT_3374 N515DRAFT_3374 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Dyella79:N515DRAFT_3374 Length = 458 Score = 442 bits (1138), Expect = e-128 Identities = 223/452 (49%), Positives = 310/452 (68%), Gaps = 2/452 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 + KV++ANRGEIA+RV+RAC LG++TVAV+S AD++ HV ADE+ IGPA + DSY Sbjct: 3 LLEKVVIANRGEIALRVLRACHSLGIKTVAVHSTADRNLKHVGLADESICIGPAPSVDSY 62 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ +I AA DA AIHPGYGFL+E A+FA +VE S F ++GP+AD + +G+K +A Sbjct: 63 LNIPRIIAAAEITDAQAIHPGYGFLSERADFAEQVEQSGFIFIGPTADVIRLMGDKVEAI 122 Query: 121 SLMQDADVPVVPGTTEP-ADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179 M+ A VP VPG+ P D ++ +A + GYPV IKA GGGGGRG++VV +E + Sbjct: 123 RAMKAAGVPCVPGSGGPLGDEVDENIRIAREIGYPVIIKAAGGGGGRGMRVVRTEAHLGN 182 Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239 K+E +A F N VY+EK+LE PRH+E+Q+LAD G+ HLGERDCS+QRRHQKV+ Sbjct: 183 AITMTKQEAKAAFGNDQVYMEKFLENPRHVEIQVLADGQGHAIHLGERDCSMQRRHQKVV 242 Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299 EEAP+P ++ +LRE+IG+ Y AGT EFL E+G FYF+E+NTRIQVEH VT Sbjct: 243 EEAPAPGITPELREQIGKVCVDACLRIGYRGAGTFEFLFENGRFYFIEMNTRIQVEHPVT 302 Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359 E +TG+D+V+ QL +A GE+L Q+D++I GH++E RINAE P+ F P+ GT+ ++ Sbjct: 303 ELITGIDLVREQLLIAGGEKLSIRQEDIKIHGHAIECRINAEDPD-SFLPSPGTVKRFEA 361 Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419 PGG G+R+D + G +I +YDSMI KLIV G DRE + R AL E IEG++ IP Sbjct: 362 PGGPGVRVDTHLYDGYKIPPNYDSMIGKLIVHGPDRETAIARMRLALAETVIEGVKCNIP 421 Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPERIEA 451 + ++ D F+ G YL++ + ++ +A Sbjct: 422 LQQRIMADVGFQHGGQNIHYLEKRMAEQKEQA 453 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: 679 Number of extensions: 23 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: 458 Length adjustment: 35 Effective length of query: 566 Effective length of database: 423 Effective search space: 239418 Effective search space used: 239418 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