Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate N515DRAFT_3374 N515DRAFT_3374 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Dyella79:N515DRAFT_3374 Length = 458 Score = 384 bits (986), Expect = e-111 Identities = 209/450 (46%), Positives = 290/450 (64%), Gaps = 6/450 (1%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 MP +V++ANRGEIA RVL+A +G+ +AV+S AD+ H ADE+ IG AP++D Sbjct: 1 MPLLEKVVIANRGEIALRVLRACHSLGIKTVAVHSTADRNLKHVGLADESICIGPAPSVD 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYLNI II AAE AIHPGYGFLSE A+FAE VE++G FIGP+++V+R + DK++ Sbjct: 61 SYLNIPRIIAAAEITDAQAIHPGYGFLSERADFAEQVEQSGFIFIGPTADVIRLMGDKVE 120 Query: 121 GKRLANMAGVPTAPGSDGPV-TSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179 R AGVP PGS GP+ +DE +++A +IGYP+++KAA GGGG G+ V + L Sbjct: 121 AIRAMKAAGVPCVPGSGGPLGDEVDENIRIAREIGYPVIIKAAGGGGGRGMRVVRTEAHL 180 Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239 + K+ A AFG +++EK+ NPRH+E Q++ D G+ + ER+C++QRR+QK Sbjct: 181 GNAITMTKQEAKAAFGNDQVYMEKFLENPRHVEIQVLADGQGHAIHLGERDCSMQRRHQK 240 Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299 ++EEAP+P + E RE + + + I Y GTFE F + FYF+E+N R+QVE Sbjct: 241 VVEEAPAPGITPELREQIGKVCVDACLRIGYRGAGTFEFLFE--NGRFYFIEMNTRIQVE 298 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359 HP TELI IDLV+ Q+ +A GE L QED+ ++ G AIE RINAED ++F S G Sbjct: 299 HPVTELITGIDLVREQLLIAGGEKLSIRQEDI--KIHGHAIECRINAEDP-DSFLPSPGT 355 Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419 V + P GPGVRVD+ + G +PP YDS++ KLIV+G RE AI ALA+ I G Sbjct: 356 VKRFEAPGGPGVRVDTHLYDGYKIPPNYDSMIGKLIVHGPDRETAIARMRLALAETVIEG 415 Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQK 449 +K I L + IM D FQ G + Y+ ++ Sbjct: 416 VKCNIPLQQRIMADVGFQHGGQNIHYLEKR 445 Lambda K H 0.317 0.135 0.385 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: 568 Number of extensions: 26 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: 509 Length of database: 458 Length adjustment: 34 Effective length of query: 475 Effective length of database: 424 Effective search space: 201400 Effective search space used: 201400 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 (21.6 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