Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_034277971.1 AMYHA_RS19150 acyl-CoA carboxylase subunit beta
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000504245.1:WP_034277971.1 Length = 512 Score = 586 bits (1510), Expect = e-172 Identities = 289/506 (57%), Positives = 368/506 (72%), Gaps = 1/506 (0%) Query: 11 REKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHKFGMEETK 70 R + + + G + QHD GK TARER++ LD +F E D +R H++ ++ Sbjct: 8 RARLRDEITAGAPAAVRRQHDLGKRTARERLELLLDPDSFIEIDMYRRHQSSSATLKSRP 67 Query: 71 LPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAPVIGLNDS 130 DGV+ G G VDGR VFV+A DFT+FGGSLG+ A KI KVMD A+ GAP+I LNDS Sbjct: 68 YT-DGVVAGSGTVDGRRVFVYAQDFTIFGGSLGQAQAAKIHKVMDHALATGAPLIALNDS 126 Query: 131 AGARIQEGVQSLGGFGEIFRRNTEASGVVPQISAIMGPCAGGAVYSPALTDFTFMVRDTS 190 GARIQEGV SL G+G IFRR+ EASGV+PQ+S IMGPCAGGA YSPAL DFTFMVR T+ Sbjct: 127 GGARIQEGVLSLHGYGGIFRRHVEASGVIPQLSVIMGPCAGGAAYSPALADFTFMVRGTA 186 Query: 191 HMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALDDIRHLLSYLPQN 250 M++TGPDV+ V+GE V+ DELGGA H S SGVA D EE LDD+R+LLS LP N Sbjct: 187 QMYLTGPDVVAAVSGERVSHDELGGADVHGSRSGVATLVYDDEESCLDDVRYLLSLLPAN 246 Query: 251 NVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSFFGVQEDFAKNIV 310 N++ PPR D + L +IVP +P +PYD+ DV+ ++D+G FF + ED+A+N++ Sbjct: 247 NLDVPPRAPAPDAEQDERPALADIVPVEPNQPYDMRDVVAEIVDDGEFFELHEDWAQNVI 306 Query: 311 VGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPILSFVDVPGFLPGT 370 G GR+ G VGIV NQP+V AG LD AS+K ARF+RFCD+FNIP+++ VDVPGFLPGT Sbjct: 307 CGLGRIGGDVVGIVGNQPQVLAGVLDRVASQKAARFVRFCDAFNIPLVTLVDVPGFLPGT 366 Query: 371 DQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGADVNYAWPTAEIA 430 +QE+ G+IRHGA+LLYAY EA+VP + VI RKAYGGAY VM S+ +G D++ AWPT EIA Sbjct: 367 EQEYAGVIRHGAQLLYAYCEASVPRIQVILRKAYGGAYIVMDSRSIGTDLSLAWPTNEIA 426 Query: 431 VMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGFVDDVIEPGDTRN 490 VMG +GAVNIL+R +L AADD RR EL+ EY +EF +P+ AA+RG VDDVI+P TR Sbjct: 427 VMGAEGAVNILHRKDLAAADDAAERRAELVAEYTDEFMHPHYAAERGLVDDVIDPAQTRA 486 Query: 491 RLIADLRMLKSKRKSQPDKKHGNIPL 516 + L ML++KR+ P++KHGNIPL Sbjct: 487 MVARGLAMLRTKRRRMPERKHGNIPL 512 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: 38 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: 516 Length of database: 512 Length adjustment: 35 Effective length of query: 481 Effective length of database: 477 Effective search space: 229437 Effective search space used: 229437 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