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_097031309.1 CRO07_RS14095 acetyl-CoA carboxylase biotin carboxylase subunit
Query= metacyc::MONOMER-13597 (509 letters) >NCBI__GCF_900207575.1:WP_097031309.1 Length = 448 Score = 374 bits (960), Expect = e-108 Identities = 198/445 (44%), Positives = 281/445 (63%), Gaps = 5/445 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV++A +EMG+ ++AV+S AD A+H + ADE+ IG A + DSYL Sbjct: 2 FEKILIANRGEIALRVIRACREMGIKSVAVHSTADADAMHVRMADESVCIGPASSTDSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 + II A E +A+HPGYGFLSENA FA+A++ GI FIGP+++ +R + DK+ K Sbjct: 62 SKAAIISACEITGAEAVHPGYGFLSENAAFAQALQDHGIEFIGPTADHIRIMGDKITAKE 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 GVP PGSDG V + A+ +A+ IG+P+++KA +GGGG G+ N ++L + Sbjct: 122 TMRALGVPCVPGSDGGVPDYEAAIGVAQSIGFPVIIKATAGGGGRGMKVARNAEELEVAF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + A AFG ++++EKY PRHIE Q+ GD G V ER+C++QRR+QK+ EE Sbjct: 182 RTARSEAKAAFGNDEVYMEKYLQRPRHIEIQVFGDGKGRAVHLGERDCSLQRRHQKVFEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 AP P + E R + + INY GT E + D +FYF+E+N RLQVEHP T Sbjct: 242 APGPVITPELRAKIGRICAEAVARINYIGAGTIEFLYED--GEFYFIEMNTRLQVEHPVT 299 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 E IF +DLV+ QI++AAG LP S + + G AIE RINAE L NFT G V + Sbjct: 300 EAIFGVDLVREQIRVAAG--LPMSLDQEALEINGHAIEVRINAE-KLPNFTPCPGKVRVF 356 Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423 P G GVR+DS + G +PPYYDSL+ KLIV+G R A+ RAL + + G+ TT Sbjct: 357 HAPGGLGVRMDSALYGGYSIPPYYDSLIGKLIVHGRDRPEALARLHRALGELIVDGVDTT 416 Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448 + L+ ++ +PD Q G ++ ++ + Sbjct: 417 VPLFHALLAEPDIQHGDYNIHWLEK 441 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: 559 Number of extensions: 24 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: 448 Length adjustment: 34 Effective length of query: 475 Effective length of database: 414 Effective search space: 196650 Effective search space used: 196650 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: 51 (24.3 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