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_057507423.1 ABB28_RS04140 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::I3R7G3 (601 letters) >NCBI__GCF_001431535.1:WP_057507423.1 Length = 455 Score = 451 bits (1159), Expect = e-131 Identities = 225/447 (50%), Positives = 307/447 (68%), Gaps = 6/447 (1%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 M K+++ANRGEIA+R++RAC LG+RTVAV+S D++ HV ADE+ IGPA + DSY Sbjct: 1 MLDKIVIANRGEIALRILRACHTLGIRTVAVHSTVDRNLKHVAMADESVCIGPAASTDSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L+ ++I AA DA AIHPGYGFL+ENA FA +VE+S F ++GP AD + +G+K +A Sbjct: 61 LNIPALIAAAEVTDAQAIHPGYGFLSENANFAERVEESGFIFIGPKADTIRLMGDKVEAI 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKA---VADDYGYPVAIKAEGGGGGRGLKVVHSEDEV 177 M+ A VP VPG+ P +D+ A +A + GYPV IKA GGGGGRG++VVH+E + Sbjct: 121 RAMKAAGVPCVPGSGGPL--GDDIVANTKIAREIGYPVIIKASGGGGGRGMRVVHAEASL 178 Query: 178 DGQFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQK 237 ET K E +A F N VY+EKYLE PRH+E+Q+LAD GN HLGERDCS+QRRHQK Sbjct: 179 KTSIETTKSEAKAAFGNGEVYMEKYLENPRHVEIQVLADGQGNAIHLGERDCSMQRRHQK 238 Query: 238 VIEEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHT 297 V+EEAP+P ++++ RE+IG+ Y AGT EFL EDG FYF+E+NTRIQVEH Sbjct: 239 VVEEAPAPGITDEAREQIGKVCVEACIRIGYRGAGTFEFLYEDGRFYFIEMNTRIQVEHP 298 Query: 298 VTEEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTY 357 VTE VTG+D+V QL++AAG++L Q D+ + GH++E RINAE E F P+ G +S + Sbjct: 299 VTEMVTGIDLVVEQLKIAAGQKLSIKQSDIVLTGHAIECRINAEDSE-TFVPSPGQISAF 357 Query: 358 DPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTV 417 PGG G+R+D + G + +YDSMI KLIV G DRE + R AL+E ++G++T Sbjct: 358 HAPGGPGVRVDTHIYAGYRVPSNYDSMIGKLIVHGPDRETAIARMRVALSEMVVDGIKTN 417 Query: 418 IPFHRLMLTDEAFREGSHTTKYLDEVL 444 + + ++ D+ F+ G YL++ L Sbjct: 418 VALQQRIMRDKGFQAGGQNIHYLEKRL 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: 659 Number of extensions: 26 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: 455 Length adjustment: 35 Effective length of query: 566 Effective length of database: 420 Effective search space: 237720 Effective search space used: 237720 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