Align Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4) (characterized)
to candidate SM_b20755 SM_b20755 propionyl-CoA carboxylase subunit beta
Query= reanno::psRCH2:GFF1050 (535 letters) >FitnessBrowser__Smeli:SM_b20755 Length = 510 Score = 248 bits (634), Expect = 3e-70 Identities = 178/523 (34%), Positives = 251/523 (47%), Gaps = 43/523 (8%) Query: 21 AMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERIDTLLDAGSAFLELAPLAAHE 80 A+LEQV RA GGG +GKL RERID LLD GS F E H Sbjct: 3 AVLEQVEARRA---EARAGGGERRIAAQHGKGKLTARERIDVLLDEGS-FEEYDMYVTHR 58 Query: 81 -----VYGEDVAAAGVVAGIGRVEGIECMIIANDATVKGGTYYPLTVKKHLRAQTVAREN 135 + G+ + GVV G G + G + + + D TV GG+ +K + +A N Sbjct: 59 SVDFGMAGQKIPGDGVVTGWGTINGRQVYVFSQDFTVLGGSLSETHAQKICKIMDMAARN 118 Query: 136 RLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQIAVVMGSCTAGGAYV 195 P I L DSGGA + E + +F A +S + IPQI+V+MG C G Y Sbjct: 119 GAPVIGLNDSGGARI---QEGVASLAGYAEVFRRNAEVSGV-IPQISVIMGPCAGGAVYS 174 Query: 196 PAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADVHCKTSGVADHYAENDEHA 255 PAM D MVR+ + +F+ GP +VK T E+VTAEELGGA H S VAD END A Sbjct: 175 PAMTDFIFMVRDSSYMFVTGPDVVKTVTNEIVTAEELGGARTHTTKSSVADGAYENDIEA 234 Query: 256 LSIARRCVANLNWRKLGQLQTRE--PRAPLY-----AADELYGVIPAQAKQPYDVREVIA 308 L R L L RE P P + L +IP A +PYD++E+I Sbjct: 235 LEHVRLLFDFL------PLNNREKPPVRPFHDDPGRLEMRLDSLIPDSAAKPYDMKELIL 288 Query: 309 RLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANN-----GILFAEAAQKGAHFIELA 363 + D ++F E +A F ++ GF + G + ++AN G L ++++K A F+ Sbjct: 289 AIADEADFFELQASFARNIITGFIRIEGQTVGVIANQPMVLAGCLDIDSSRKAARFVRFC 348 Query: 364 CQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGSFGAGNYG 423 IP+L L ++ GF+ G E GG+ KHGAKL+ A + A VP T++ ++G Sbjct: 349 DAFSIPILTLVDVPGFLPGTAQEYGGVIKHGAKLLFAYSQATVPMVTLITRKAYGGAYDV 408 Query: 424 MCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAAIKQPILE 483 M + + WP A IAVMG + A +L + LGD A I E Sbjct: 409 MASKHIGADVNYAWPTAEIAVMGAKGATEILYR----------SELGDP--AKIAARTKE 456 Query: 484 QYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPIE 526 ER +P+ ++ R + D VI P +R + A ++ N +E Sbjct: 457 YEERFANPFVAAERGFIDEVIMPHSSRRRIARAFASLRNKQVE 499 Lambda K H 0.321 0.136 0.405 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: 636 Number of extensions: 29 Number of successful extensions: 5 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: 535 Length of database: 510 Length adjustment: 35 Effective length of query: 500 Effective length of database: 475 Effective search space: 237500 Effective search space used: 237500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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