Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_022601570.1 NSB1T_RS24085 acyl-CoA carboxylase subunit beta
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000473955.1:WP_022601570.1 Length = 511 Score = 619 bits (1597), Expect = 0.0 Identities = 313/505 (61%), Positives = 382/505 (75%), Gaps = 6/505 (1%) Query: 12 EKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETKL 71 E+ A GG DRI QH GK+TARERI+ LD +F E D+F HR +GM+ ++ Sbjct: 13 ERNRAAEMAGGADRIGKQHAAGKLTARERIELLLDPASFNELDKFVVHRCKDYGMDGARI 72 Query: 72 PGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDSA 131 PGDGV++G+G ++GR VFV+A+DFTVFGG+L A KI KV D A++ GAPVI LNDS Sbjct: 73 PGDGVVSGYGRIEGRLVFVYAYDFTVFGGTLSAENARKIMKVQDLALKNGAPVIALNDSG 132 Query: 132 GARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTSH 191 GARIQEGV+SL G+ IF RNT ASGV+PQISAI+GPCAGGA YSPALTDF FMVR SH Sbjct: 133 GARIQEGVESLSGYAGIFFRNTMASGVIPQISAILGPCAGGACYSPALTDFIFMVRGYSH 192 Query: 192 MFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQNN 251 MF+TGPDV+K VT E V +ELGGA TH S SGVAHF D+E++ + +IR LLS+LP NN Sbjct: 193 MFVTGPDVVKAVTHELVGKEELGGAVTHASVSGVAHFLGDSEKEVILEIRELLSFLPANN 252 Query: 252 VEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIVV 311 +ED P V DD R L E++PD P PYD+ +V+ V+D+G FF V DFAKNIV+ Sbjct: 253 MEDAPCVPCRDDIRREVTGLREVIPDDPNIPYDMKEVIVPVVDDGYFFEVMPDFAKNIVI 312 Query: 312 GFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGTD 371 GF RL G +VGIVANQP AG LDI+AS+K ARFIRFCD FNIP+++F DVPGFLPGT Sbjct: 313 GFARLGGRTVGIVANQPAFLAGVLDIDASDKAARFIRFCDCFNIPLVTFEDVPGFLPGTV 372 Query: 372 QEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIAV 431 QEHNGIIRHGAK++YA++EATVP +T+ITRKAYGGAY VMASK GAD+N A+P AEIAV Sbjct: 373 QEHNGIIRHGAKVVYAFAEATVPKVTLITRKAYGGAYIVMASKLTGADINLAFPNAEIAV 432 Query: 432 MGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRNR 491 MG +GAVNIL+R+ AD + +R EL EEYRE FANP+ AA+ G++D+VI P TR + Sbjct: 433 MGAEGAVNILFRN----AD--NEKRAELTEEYRERFANPFRAAELGYIDEVILPEQTRAK 486 Query: 492 LIADLRMLKSKRKSQPDKKHGNIPL 516 LIA L M ++K S P KKHGN+PL Sbjct: 487 LIAALEMAQNKNVSNPPKKHGNMPL 511 Lambda K H 0.318 0.138 0.407 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: 801 Number of extensions: 28 Number of successful extensions: 4 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: 516 Length of database: 511 Length adjustment: 35 Effective length of query: 481 Effective length of database: 476 Effective search space: 228956 Effective search space used: 228956 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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