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 3607308 Dshi_0723 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Dino:3607308 Length = 681 Score = 380 bits (975), Expect = e-109 Identities = 199/466 (42%), Positives = 292/466 (62%), Gaps = 23/466 (4%) Query: 4 FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63 F ++L+ANRGEIA RV+K ++MG+ +A+YS+AD+ A+H + ADEA +IG +PA SY+ Sbjct: 2 FKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYI 61 Query: 64 NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123 I+ ++DA + +A+HPGYGFLSEN FAEA+EK G+ FIGP + + + DK+ K+ Sbjct: 62 VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121 Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183 +A A V T PG G + DEA+K++ +IGYP+M+KA++GGGG G+ N + + + Sbjct: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGF 181 Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243 + +K A +FG +FIEK+ PRHIE Q++ D +GN + EREC+IQRRNQK++EE Sbjct: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEE 241 Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303 APSP L R++M E + + Y + GT E D R+FYFLE+N RLQVEHP T Sbjct: 242 APSPFLDEATRKAMGEQSCALAQAVGYASAGTVE-FIVDGDRNFYFLEMNTRLQVEHPVT 300 Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363 ELI +DLV+ I++AAGE LP +Q+D+ + G AIE R+ AED NF S G +T Y Sbjct: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVT--LTGWAIENRLYAEDPYRNFLPSIGRLTRY 358 Query: 364 R-------------------EPTGP-GVRVDSGIESGSYVPPYYDSLVSKLIVYGESREY 403 R P+GP VR D+G+ G + YYD +++KL +G R Sbjct: 359 RPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPA 418 Query: 404 AIQAGIRALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQK 449 AI+A AL +++ GI + +M P F +G+ +T++I ++ Sbjct: 419 AIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQ 464 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: 754 Number of extensions: 34 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: 681 Length adjustment: 37 Effective length of query: 472 Effective length of database: 644 Effective search space: 303968 Effective search space used: 303968 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