Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_101588272.1 BJEO58_RS04965 ATP-grasp domain-containing protein
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_900169175.1:WP_101588272.1 Length = 1074 Score = 239 bits (611), Expect = 3e-67 Identities = 153/494 (30%), Positives = 240/494 (48%), Gaps = 10/494 (2%) Query: 4 EDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHK 63 E I+E+R + EEA K GG ++A QH+ G++TARERI D+G+F E + + Sbjct: 562 EQEIEEIRRRHEEAYKHGGAAKVARQHESGRLTARERIAALADEGSFDEIGPLAGYGEYD 621 Query: 64 FGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAP 123 + ++G G + GR + DF++ GGS +K A E+ P Sbjct: 622 EDGNLLGVRPSNFLSGTGRIRGRRALLGVDDFSIRGGSGDAAVHQKQVFTEQLAGEMRVP 681 Query: 124 VIGLND--SAGARIQEGVQSLGGFGEI---FRRNTEASGVVPQISAIMGPCAGGAVYSPA 178 ++ + D S G +++ + + + + + + +P +S GP G Sbjct: 682 MVRVLDGASGGGSVKKVLTAQAMYLPVNPGWDHVVDNMSRIPVVSVCAGPTVGLGAARFV 741 Query: 179 LTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQALD 238 ++ F MV+ +F GP V+K TGE++ D LGG H + V F D EE A + Sbjct: 742 MSHFGVMVQGIGQLFTAGPPVVKAATGEDLDKDGLGGEAVHRTNGTVERFVPD-EETAFE 800 Query: 239 DIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEGSF 298 +R LSYLP + E PP E D +R + L VP PR+ Y I +L+ V D GS Sbjct: 801 VVRDFLSYLPSSVDELPPVAENSDPVDRSEESLAAAVPRNPRQIYAIEPILHAVFDHGSV 860 Query: 299 FGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIPIL 358 F E + RLDG VG+V P A TL E ++ R + C++F++P++ Sbjct: 861 FRFAE-YGDGTYTALARLDGRPVGVVTADPSQGA-TLSREGAQAVERLVDICEAFHLPLV 918 Query: 359 SFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMASKHLGA 418 S D G G E + IR GA+ + A +A +P +I R+ YG + ++H A Sbjct: 919 SLTDQAGMTIGLQAEKDATIRAGARAIAAIYQARIPQAEIILRRVYGVGGAGIVNRH-RA 977 Query: 419 DVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAADRGF 478 ++AWP+ + + PQG + +R EL A DDP+ R E+ E E ++ + A+ Sbjct: 978 VRSWAWPSGDWGSLPPQGGIEAAFRAELAAHDDPEKRLAEITHE-MELVSSRFRTAETFS 1036 Query: 479 VDDVIEPGDTRNRL 492 V D+I+P TR RL Sbjct: 1037 VQDIIDPRTTRRRL 1050 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: 1401 Number of extensions: 76 Number of successful extensions: 8 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: 1074 Length adjustment: 40 Effective length of query: 476 Effective length of database: 1034 Effective search space: 492184 Effective search space used: 492184 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: 55 (25.8 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