Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_057507423.1 ABB28_RS04140 acetyl-CoA carboxylase biotin carboxylase subunit
Query= BRENDA::Q9I299 (655 letters) >NCBI__GCF_001431535.1:WP_057507423.1 Length = 455 Score = 419 bits (1076), Expect = e-121 Identities = 222/434 (51%), Positives = 294/434 (67%), Gaps = 4/434 (0%) Query: 8 IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67 + ++++ANRGEIA R++R+ LGI +VAVHS +DR+ +HVA AD +V +G A DSYL Sbjct: 2 LDKIVIANRGEIALRILRACHTLGIRTVAVHSTVDRNLKHVAMADESVCIGPAASTDSYL 61 Query: 68 RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127 +IAAA + AQAIHPGYGFLSENA+FA EE+G +F+GP A I MG K A Sbjct: 62 NIPALIAAAEVTDAQAIHPGYGFLSENANFAERVEESGFIFIGPKADTIRLMGDKVEAIR 121 Query: 128 LMEEAGVPLVPGYHGE-AQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M+ AGVP VPG G D+ + A IGYPV++KA+ GGGG+GM+VV EA L + Sbjct: 122 AMKAAGVPCVPGSGGPLGDDIVANTKIAREIGYPVIIKASGGGGGRGMRVVHAEASLKTS 181 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 + + + EAKAAFG+ + +EKYL PRHVEIQV AD G+ ++L ERDCS+QRRHQKVVE Sbjct: 182 IETTKSEAKAAFGNGEVYMEKYLENPRHVEIQVLADGQGNAIHLGERDCSMQRRHQKVVE 241 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAPAPG+ E R +G+ V A IGY GAGT EFL ++ G+F+F+EMNTR+QVEHPVT Sbjct: 242 EAPAPGITDEAREQIGKVCVEACIRIGYRGAGTFEFLYED-GRFYFIEMNTRIQVEHPVT 300 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E +TG+DLV Q+++A G+ L + Q + L GHAIE R+ AED E F+P+ G++ + Sbjct: 301 EMVTGIDLVVEQLKIAAGQKLSIKQSDIVLTGHAIECRINAEDSE-TFVPSPGQISAF-H 358 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 A GPG RVD+ + G V YD M+ KLI G RE A R+ L+E V G++TN+ Sbjct: 359 APGGPGVRVDTHIYAGYRVPSNYDSMIGKLIVHGPDRETAIARMRVALSEMVVDGIKTNV 418 Query: 427 AFLRRILGHPAFAA 440 A +RI+ F A Sbjct: 419 ALQQRIMRDKGFQA 432 Lambda K H 0.319 0.135 0.397 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: 690 Number of extensions: 20 Number of successful extensions: 4 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: 655 Length of database: 455 Length adjustment: 35 Effective length of query: 620 Effective length of database: 420 Effective search space: 260400 Effective search space used: 260400 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 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