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 WP_057507601.1 ABB28_RS05090 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_001431535.1:WP_057507601.1 Length = 660 Score = 368 bits (944), Expect = e-106 Identities = 200/495 (40%), Positives = 296/495 (59%), Gaps = 7/495 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F+++L+ANRGEIA RV+ + +G+ +AVYS+AD+ A H + ADEA IG APA +SYL Sbjct: 2 FTKILIANRGEIACRVIATCRRLGIATVAVYSDADRTARHVRLADEAIAIGPAPAAESYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + I++AA ++ AIHPGYGFLSENA FAEA AG+ FIGP + +R + DK K Sbjct: 62 RADVILEAARRSGAQAIHPGYGFLSENAAFAEACAAAGVVFIGPPASAIRAMGDKSAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L AGVP PG G A+ IGYP+++KA++GGGG G+ RVD+ ++ Sbjct: 122 LMQQAGVPLTPGYHGDDQDPQFLRGQADAIGYPVLIKASAGGGGKGMRRVDDSAAFIEAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 +R A AFG + +EKY + PRHIE Q+ GD +GN V +ER+C++QRR+QK++EE Sbjct: 182 ASCQREARSAFGNDHVLVEKYVLRPRHIEIQVFGDGHGNVVHLFERDCSVQRRHQKVLEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP+P + E R +M + + + + Y GT E S DFYF+E+N RLQVEHP T Sbjct: 242 APAPGMTAERRAAMGKAAVDAARAVGYVGAGTVEFIASP-DGDFYFMEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E I DLV Q+++AAG+ LP Q++L + G A+E R+ AEDA F S G + + Sbjct: 301 EFITGTDLVAWQLRVAAGQPLPKRQDEL--AIGGHALEARLYAEDADKGFLPSIGTLRHL 358 Query: 364 R-EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422 R P VRVD+G+E G + P+YD +++KLIV+ R+ A++ +ALAD ++ G+ T Sbjct: 359 RLPPESAHVRVDTGVEQGDTITPFYDPMIAKLIVWDVDRDAALRRMQQALADCQVVGVTT 418 Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEI--KAAIAAEIQSRGLLRTS 480 + ++ F + K T+ I ++ D + + AAI A + + Sbjct: 419 NAGFLRRLVGTDSFAQAKLDTALIEREQDALAAPAAGEAALWTLAAIGA-VVTTARAAVD 477 Query: 481 STDNKGKAQSKSGWK 495 + D + Q++ GW+ Sbjct: 478 ARDPRSPWQAQDGWR 492 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: 760 Number of extensions: 33 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: 660 Length adjustment: 36 Effective length of query: 473 Effective length of database: 624 Effective search space: 295152 Effective search space used: 295152 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 Apr 09 2024. 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