Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate N515DRAFT_3374 N515DRAFT_3374 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= BRENDA::Q9I299 (655 letters) >FitnessBrowser__Dyella79:N515DRAFT_3374 Length = 458 Score = 430 bits (1105), Expect = e-125 Identities = 229/432 (53%), Positives = 300/432 (69%), Gaps = 4/432 (0%) Query: 8 IQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYL 67 ++++++ANRGEIA RV+R+ +LGI +VAVHS DR+ +HV AD ++ +G A DSYL Sbjct: 4 LEKVVIANRGEIALRVLRACHSLGIKTVAVHSTADRNLKHVGLADESICIGPAPSVDSYL 63 Query: 68 RGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKA 127 RIIAAA + AQAIHPGYGFLSE ADFA E++G +F+GP A I MG K A Sbjct: 64 NIPRIIAAAEITDAQAIHPGYGFLSERADFAEQVEQSGFIFIGPTADVIRLMGDKVEAIR 123 Query: 128 LMEEAGVPLVPGYHGEAQD-LETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186 M+ AGVP VPG G D ++ R A IGYPV++KAA GGGG+GM+VV EA L A Sbjct: 124 AMKAAGVPCVPGSGGPLGDEVDENIRIAREIGYPVIIKAAGGGGGRGMRVVRTEAHLGNA 183 Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246 ++ ++EAKAAFG+ ++ +EK+L PRHVEIQV AD GH ++L ERDCS+QRRHQKVVE Sbjct: 184 ITMTKQEAKAAFGNDQVYMEKFLENPRHVEIQVLADGQGHAIHLGERDCSMQRRHQKVVE 243 Query: 247 EAPAPGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHPVT 306 EAPAPG+ ELR +G+ V A IGY GAGT EFL E G+F+F+EMNTR+QVEHPVT Sbjct: 244 EAPAPGITPELREQIGKVCVDACLRIGYRGAGTFEFLF-ENGRFYFIEMNTRIQVEHPVT 302 Query: 307 EAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYRE 366 E ITG+DLV Q+ +A GE L + QE + ++GHAIE R+ AEDP+ FLP+ G + + E Sbjct: 303 ELITGIDLVREQLLIAGGEKLSIRQEDIKIHGHAIECRINAEDPD-SFLPSPGTVKRF-E 360 Query: 367 AAAGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNL 426 A GPG RVD+ + +G ++ P YD M+ KLI G RE A R+ LAET + G++ N+ Sbjct: 361 APGGPGVRVDTHLYDGYKIPPNYDSMIGKLIVHGPDRETAIARMRLALAETVIEGVKCNI 420 Query: 427 AFLRRILGHPAF 438 +RI+ F Sbjct: 421 PLQQRIMADVGF 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: 727 Number of extensions: 27 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: 458 Length adjustment: 36 Effective length of query: 619 Effective length of database: 422 Effective search space: 261218 Effective search space used: 261218 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: 53 (25.0 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