Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_088756563.1 CEJ45_RS18815 urea carboxylase
Query= SwissProt::Q5LUF3 (681 letters) >NCBI__GCF_002213425.1:WP_088756563.1 Length = 1207 Score = 390 bits (1001), Expect = e-112 Identities = 216/461 (46%), Positives = 290/461 (62%), Gaps = 22/461 (4%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+ +LIANRG IACR+++T R + ++ V +YS+AD +LHV AD A+ +G PA Q+Y Sbjct: 1 MFDHLLIANRGVIACRILRTLRTLDVTGVCVYSEADLGSLHVLQADRAISLGEGPAAQTY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 +V+DK++AA R +GAQA+HPGYGFLSEN+ FAEA EA G+ FVGP + G K T++ Sbjct: 61 LVVDKILAAARDSGAQAIHPGYGFLSENAAFAEACEAAGIAFVGPTPAQLRIFGLKHTAR 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 +A+E V + G L+E+ +A+ + ++GYPVM+K++AGGGG GMR+ +D E + Sbjct: 121 ALAREQGVPMLEG-TDLLENIGDALAAAARVGYPVMLKSTAGGGGIGMRVCRSDAELGDA 179 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 F S + N+F D +FIEK++ + RH+E+QV D G I LG R+CS+QRRNQKV+E Sbjct: 180 FDSVRRLGQNNFSDAGVFIEKYIERARHLEVQVFGDGRGEVIALGVRDCSVQRRNQKVLE 239 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDG-QKNFYFLEMNTRLQVEHPV 299 E P+P L E A+ A+ LAKAV Y SAGTVEF+ D FYFLE+NTRLQVEH V Sbjct: 240 ETPAPNLPEGMADALCAAAIKLAKAVNYRSAGTVEFVYDSLAGQFYFLEVNTRLQVEHGV 299 Query: 300 TELITGVDLVEQMIRVAAGE--PLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTR 357 TE + GVDLV MI +AAG+ PL+ ++ G AI+ RLYAEDP R F P G LT Sbjct: 300 TEQVWGVDLVRWMIELAAGDLPPLAQLAASLQPRGHAIQARLYAEDPGRQFQPCPGLLTA 359 Query: 358 YRPPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRA 417 PA + A+R DT V G EI Y+DPMIAKL +W PTR Sbjct: 360 VDFPA------------------ADGQALRIDTWVEAGCEIPPYFDPMIAKLISWQPTRE 401 Query: 418 AAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTT 458 AA A+ AL + G+ N +L ++D F G T Sbjct: 402 AARVALNSALRETALYGVETNQHYLRQILDDVPFARGQPWT 442 Score = 42.4 bits (98), Expect = 1e-07 Identities = 20/64 (31%), Positives = 36/64 (56%) Query: 618 PMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKGVVAKINASAGNSLAVDDVI 677 P+ G + +V V GQ V +G+ L +E+MKME + A + G+VA++ G+ + + Sbjct: 1137 PIAGNLWQVKVSPGQRVAQGELLMILESMKMEINITAPEAGIVAEVRVQPGSPVRAGQCV 1196 Query: 678 MEFE 681 + E Sbjct: 1197 LVME 1200 Lambda K H 0.317 0.134 0.387 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: 1846 Number of extensions: 87 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 681 Length of database: 1207 Length adjustment: 43 Effective length of query: 638 Effective length of database: 1164 Effective search space: 742632 Effective search space used: 742632 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: 56 (26.2 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