Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate RR42_RS01335 RR42_RS01335 methylmalonyl-CoA carboxyltransferase
Query= SwissProt::I3R7F1 (516 letters) >FitnessBrowser__Cup4G11:RR42_RS01335 Length = 515 Score = 272 bits (696), Expect = 2e-77 Identities = 169/523 (32%), Positives = 272/523 (52%), Gaps = 16/523 (3%) Query: 1 MTMEDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHR 60 M+ + IDEL +++ A + GG D++ D GK+T RERID D G+FRE Sbjct: 1 MSWQPEIDELAYRKQLAAQLGGPDKVKRHKDAGKLTVRERIDAIADAGSFREVGALTGSG 60 Query: 61 NHKFGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEV 120 + L ++ G +VDGR V + DFTV GG+ EK+ A ++ Sbjct: 61 QYDSNGRLVGLTPANLVMGRAKVDGRPVVLVGDDFTVRGGANDGAVGEKLIHAEKMAHDL 120 Query: 121 GAPVIGLNDSAGARIQEGVQSLGGFG-------EIFRRNTEASGVVPQISAIMGPCAGGA 173 P++ L D G V+++ G ++++ E +VP +S +G AG Sbjct: 121 RLPMVRLVDGTGGG--GSVRNIENKGYTNIPTMKVWQHVVENMSLVPVVSLALGSVAGMG 178 Query: 174 VYSPALTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTE 233 A + ++ MV+ T+ +F GP V+ + G+ + +ELGG+ HT +GV +E Sbjct: 179 AARVAASHYSVMVKGTAQLFNAGPPVVARI-GQVLEKNELGGSQIHTR-NGVVDDEVASE 236 Query: 234 EQALDDIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVL 293 E+A R LSYLP + E PPRVEP DDP R + L +P R Y + ++ ++ Sbjct: 237 EEAFARARRFLSYLPGSVHELPPRVEPTDDPARRDEWLLSAIPRDSRSVYKVRPIVETLV 296 Query: 294 DEGSFFGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSF 353 D+GSFF + + + IV G R+DG V +VA+ P G D +EK RF+ ++F Sbjct: 297 DQGSFFEMGRHWGRAIVTGLARVDGWPVAVVASDPYHYGGGWDGPTAEKFIRFVDLAEAF 356 Query: 354 NIPILSFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAYDVMAS 413 ++P+++ VD+ GF G + E G +R+G + L A +AT P +VI R+AYG A Sbjct: 357 HLPVINMVDIAGFQIGLEAEKAGTMRYGVRALAAVYQATTPWCSVILRRAYGVA--AAGH 414 Query: 414 KHLGA-DVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYT 472 +H+G + YAWP+ + +G + + Y+ E+E ADDP +R E IE+ +P+ Sbjct: 415 QHMGRFNFRYAWPSGNWGSLPIEGGLEVAYKAEIEGADDPVQKRAE-IEQRVRSLTSPFR 473 Query: 473 AADRGFVDDVIEPGDTRNRLIADLRMLKSKRKSQPDKKHGNIP 515 +A+ V+D+I+P DTR+ L+ + L + + +K G P Sbjct: 474 SAEAFVVEDIIDPRDTRS-LLCEFANLAAPLREPGVRKFGIRP 515 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: 704 Number of extensions: 31 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: 515 Length adjustment: 35 Effective length of query: 481 Effective length of database: 480 Effective search space: 230880 Effective search space used: 230880 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 17 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