Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_012043673.1 BBTA_RS16720 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >NCBI__GCF_000015165.1:WP_012043673.1 Length = 519 Score = 276 bits (707), Expect = 1e-78 Identities = 171/519 (32%), Positives = 276/519 (53%), Gaps = 20/519 (3%) Query: 1 MTMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHR 60 M+ + ++EL + A + GG D++ QHD+G++T RERID +D G+F E Sbjct: 1 MSWQPELEELARREAFAREMGGPDKVKRQHDQGRLTVRERIDGVVDAGSFHEIGAVAGLG 60 Query: 61 NHKFGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEV 120 + E + + G +DGRTV V DFTV GGS A K + A + Sbjct: 61 EYDEQGELKHVTPANCVFGRARIDGRTVVVVGDDFTVRGGSADASIAAKPLMAEEMAHDF 120 Query: 121 GAPVIGLNDSAGARIQ------EGVQSL-GGFG--EIFRRNTEASGVVPQISAIMGPCAG 171 P+I + + +G +G +L GG G +R TE +VP ++ +G AG Sbjct: 121 RLPIIRIIEGSGGGGSVKTIETKGAANLPGGIGGNRWYRYTTENMSLVPVVALGLGSVAG 180 Query: 172 GAVYSPALTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATD 231 A + ++ M + ++ MF+ GP V+K + G+++ ELGGA T GV H A D Sbjct: 181 LGAARLAASHYSVMTKQSA-MFVAGPPVVKRL-GQDLGKMELGGADIQTRAGGVDH-AVD 237 Query: 232 TEEQALDDIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNG 291 TE +A R LSYLP + E PP + DDP+R ++L VP R+ Y + ++ Sbjct: 238 TEAEAFACARRFLSYLPSSVYELPPTLPCTDDPQRTDEQLISAVPRDRRRVYKMRPIIES 297 Query: 292 VLDEGSFFGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCD 351 V+D GSFF V +++ + I++G RL+G +V ++A+ P G+ +A +K R++ F + Sbjct: 298 VVDSGSFFEVAQNYGRPIIIGLARLEGRAVMVLASDPYHYGGSWTADACQKVIRWVDFAE 357 Query: 352 SFNIPILSFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVM 411 +F++PI+ +D PGF+ G + E IRHG + + A +++TVP TVI R ++G V Sbjct: 358 TFHLPIVYLMDCPGFMVGLEAEKAATIRHGVRAMAAVNQSTVPWCTVIVRNSFG----VA 413 Query: 412 ASKHLGAD---VNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFA 468 H AD + YAWP+A + +G + YR E++AA DP A+ E IEE + Sbjct: 414 GVVHQPADRFSIRYAWPSAYWGSLPLEGGIEAAYRAEIDAAPDPKAKLKE-IEERLNKLR 472 Query: 469 NPYTAADRGFVDDVIEPGDTRNRLIADLRMLKSKRKSQP 507 +P+ +A++ +V+++I+P TR L R+ + R P Sbjct: 473 SPFRSAEKFWVEEIIDPRKTRALLCEFARLAEPLRTVGP 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: 736 Number of extensions: 37 Number of successful extensions: 6 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: 519 Length adjustment: 35 Effective length of query: 481 Effective length of database: 484 Effective search space: 232804 Effective search space used: 232804 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