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 HSERO_RS23460 HSERO_RS23460 3-methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__HerbieS:HSERO_RS23460 Length = 671 Score = 340 bits (872), Expect = 9e-98 Identities = 193/507 (38%), Positives = 283/507 (55%), Gaps = 22/507 (4%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV + +G+ +AVYS+AD A H DE+ +G APA +SYL Sbjct: 2 FTKILIANRGEIACRVAATARRLGIATVAVYSDADARAKHVAACDESVRLGPAPARESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E II AA AIHPGYGFLSENA FA+A +AG+ FIGP + + + K K Sbjct: 62 CAEKIIAAALATGAQAIHPGYGFLSENAGFAQACAQAGLVFIGPPASAIEAMGSKAAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L A VP PG G A++IGYP+++KA++GGGG G+ V+ + Sbjct: 122 LMEQAAVPLVPGYHGEEQESGLLHSQADRIGYPVLLKASAGGGGKGMRVVERSEDFDAAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 KR A +FG + +EKY PRHIE Q+ D +G+ V +ER+C++QRR+QK++EE Sbjct: 182 ASCKREAIASFGDDRVLVEKYLTRPRHIEIQVFADGHGHCVYLFERDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P + E R +M E + + + Y GT E ++ FYF+E+N RLQVEHP T Sbjct: 242 APAPGMSEERRAAMGEAAVAAARAVGYVGAGTVE-FIANQDGSFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E+I +DLV+ Q+++AAG+ LP QE L R+ G AIE RI AE+ F + G +T Sbjct: 301 EMITGLDLVEWQLRVAAGQALPLKQEQL--RIHGHAIEARIYAENPEKGFLPAIGTLTRM 358 Query: 364 RE---------PTGPG----VRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIR 410 R + PG VR+D+G+ G + P+YD +++KLIV+G R+ A++ R Sbjct: 359 RSAAAVEFRLGQSAPGDPAHVRIDAGVREGDAISPFYDPMIAKLIVWGPDRDAALRNMQR 418 Query: 411 ALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV--KYLREQEEIKAAIA 468 ALA Y++ G+ T I + ++ F T I + D + E + AIA Sbjct: 419 ALAQYQVVGLATNIAFLQRLVAGQAFSTAALDTGLIERHRDTLFPPPSSPDTETLALAIA 478 Query: 469 AEIQSRGLLRTSSTDNKGKAQSKSGWK 495 A +Q + + ++GW+ Sbjct: 479 AILQQ----EHAQAERSDPWSQRNGWR 501 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: 711 Number of extensions: 28 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: 509 Length of database: 671 Length adjustment: 36 Effective length of query: 473 Effective length of database: 635 Effective search space: 300355 Effective search space used: 300355 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: 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