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 5210790 Shew_3218 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__PV4:5210790 Length = 1516 Score = 280 bits (715), Expect = 3e-79 Identities = 168/456 (36%), Positives = 248/456 (54%), Gaps = 14/456 (3%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYA---DEAYYIGKAP 57 M P +VLV RG A ++++ + + + V S+ D +V D+ IG Sbjct: 937 MKPIDKVLVHARGCTAVKLIRKAHDNNIKVVLVASDPDMTSVPADMLNENDKLVCIGGNT 996 Query: 58 ALDSYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKD 117 + +SYLN ++ AE VDA+HPG GFLSE+ +FA G+ F+GPS M + + Sbjct: 997 SDESYLNAYSVLKVAEYEQVDALHPGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGN 1056 Query: 118 KLDGKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQD 177 K + + + VP PGS G +T+ ++A+ +A +IGYP+++KA GGGG GI V + Sbjct: 1057 KSNAIKTSQSQNVPVVPGSHGILTNAEQAVNVANEIGYPVLLKAVQGGGGKGIQVVQRPE 1116 Query: 178 QLMDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRN 237 ++ ++++ A AFG DL++EKY + RHIE QL+ DK+GN V R+C++QR N Sbjct: 1117 DMISLFQKTSTEAAAAFGNGDLYLEKYVTSLRHIEVQLLRDKFGNTKVLGLRDCSVQRNN 1176 Query: 238 QKLIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQ 297 QK+IEE+ S L E ++ + E G +Y GT E ++ + + YF+E+N RLQ Sbjct: 1177 QKVIEESGSTMLPEELKQQVMEYTRALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQ 1236 Query: 298 VEHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTG-- 355 VEHP TE ID+V +AAG S EDL + G AIE R+ AE A + G Sbjct: 1237 VEHPVTEATSGIDIVSAGFDIAAGR----SIEDLEPQEIGYAIEVRVTAEKAALDSNGVL 1292 Query: 356 ----SSGFVTYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRA 411 G +T P + + S G V PYYDSL++++I GESRE I Sbjct: 1293 QLLPHPGMITECVIPERDDIEIISIAGEGKEVSPYYDSLIAQIICRGESREDVINKLHDY 1352 Query: 412 LAD-YKIGGIKTTIELYKWIMQDPDFQEGKFSTSYI 446 LA+ I GI T I L I++D F EG + T+Y+ Sbjct: 1353 LANQVVIKGIATNIPLLTRILKDGTFNEGVYDTNYL 1388 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: 1491 Number of extensions: 69 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: 1516 Length adjustment: 42 Effective length of query: 467 Effective length of database: 1474 Effective search space: 688358 Effective search space used: 688358 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: 56 (26.2 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