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 3607893 Dshi_1301 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Dino:3607893 Length = 661 Score = 322 bits (825), Expect = 3e-92 Identities = 183/452 (40%), Positives = 264/452 (58%), Gaps = 9/452 (1%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F R+L+ANRGEIA RV+ + +G+ +AV+S+ D A H AD A +G A DSYL Sbjct: 2 FERILIANRGEIACRVIDTCRRLGVQTVAVHSDVDAGARHVAMADMAVNLGGAAPRDSYL 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 E II AA +AIHPGYGFLSEN +F EAV AG+ FIGPS+ +R + K K Sbjct: 62 RGEAIIAAARATGAEAIHPGYGFLSENPDFVEAVAAAGLVFIGPSAAAIRAMGLKDAAKA 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 L AGVP PG G AE IGYP+++KA +GGGG G+ RV+ + Sbjct: 122 LMAEAGVPVVPGYQGADQDPARLAAEAEAIGYPVLIKAVAGGGGKGMRRVEGPEGFAGAL 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 E + A AFG + +EKY PRHIE Q+ GD V +ER+C++QRR+QK+IEE Sbjct: 182 EAARAEARGAFGNDHVLLEKYVATPRHIELQVFGDG-ARAVHLFERDCSLQRRHQKVIEE 240 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFE--TAFSDVSRD--FYFLELNKRLQVE 299 AP+P + E R +M ++ + I Y GT E SD R F+F+E+N RLQVE Sbjct: 241 APAPGMTPEMRAAMGAAAVRAAEAIGYAGAGTVEFIVDASDGLRPDRFWFMEMNTRLQVE 300 Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGF 359 HP TE + +DLV Q+++A+GE LP QEDL+ +RG A E R+ AED F ++G Sbjct: 301 HPVTEAVTGVDLVAWQLRVASGEPLPARQEDLS--LRGHAFEARLYAEDVPKGFLPATGR 358 Query: 360 VTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGG 419 +T+ P R+++G+ +G + P+YD +++KL+V+G +R+ A++ R LA ++ G Sbjct: 359 LTHLAFPA--DARIETGVRAGDEISPWYDPMIAKLVVHGPTRQSALRKLDRVLAGCEVAG 416 Query: 420 IKTTIELYKWIMQDPDFQEGKFSTSYISQKTD 451 T + + + + F G+ T I ++ + Sbjct: 417 SVTNLAFLRALARHGGFFAGEVDTGLIDREVE 448 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: 776 Number of extensions: 41 Number of successful extensions: 6 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: 661 Length adjustment: 36 Effective length of query: 473 Effective length of database: 625 Effective search space: 295625 Effective search space used: 295625 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