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 RR42_RS25130 RR42_RS25130 pyruvate carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Cup4G11:RR42_RS25130 Length = 1167 Score = 347 bits (891), Expect = 1e-99 Identities = 185/478 (38%), Positives = 285/478 (59%), Gaps = 20/478 (4%) Query: 3 PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPA-LDS 61 P +L+ANR EIA RV++A EM + +A+YS+ D+ A+H ADE+Y +G+ L + Sbjct: 5 PIKSLLIANRSEIAIRVMRAAAEMNIRTVAIYSKEDRLALHRFKADESYLVGEGKKPLAA 64 Query: 62 YLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDG 121 YL+I+ I+ A +A VDAIHPGYGFLSEN +FA+AV AGI +IGPS EVMRK+ +K+ Sbjct: 65 YLDIDDILRIARQAKVDAIHPGYGFLSENPDFAQAVMDAGIRWIGPSPEVMRKLGNKVAA 124 Query: 122 KRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181 + A AGVP P +D +DE +LA IGYP+M+KA+ GGGG G+ ++N+ L Sbjct: 125 RNAAIEAGVPVMPATDPLPRDLDECKRLAAGIGYPLMLKASWGGGGRGMRMLENEQDLET 184 Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241 +R A AFG ++++EK N RH+E Q +GD +GN V +ER+CT+QRRNQK++ Sbjct: 185 ALPAARREALSAFGNDEVYVEKLVRNARHVEVQALGDAHGNLVHLYERDCTVQRRNQKVV 244 Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHP 301 E AP+P L R ++ + ++ + + Y GT E S FYF+E+N R+QVEH Sbjct: 245 ERAPAPYLDDAGRAALCDAAMRLMRAVGYTHAGTIEFLMDADSGQFYFIEVNPRIQVEHT 304 Query: 302 TTELIFRIDLVKLQIKLAAGEHLPFSQ-----------------EDLNKRVRGTAIEYRI 344 TEL+ +D+VK QI++ G H+ ++ E + G A++ RI Sbjct: 305 VTELVTGVDIVKAQIRITEGGHIGMTENTRDADGKIVVRAAGVPEQAGISLNGHALQCRI 364 Query: 345 NAEDALNNFTGSSGFVTYYREPTGPGVRVDSGIE-SGSYVPPYYDSLVSKLIVYGESREY 403 ED N F G ++ YR G GVR+D+G G+ + PYYDSL+ K+ + + Sbjct: 365 TTEDPENGFLPDYGRLSAYRSAAGFGVRLDAGTAYGGAVITPYYDSLLVKVTTWAPTAPE 424 Query: 404 AIQAGIRALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQE 461 +I+ RAL +++I G+ + ++ + ++ P F+ G +T +I KT + + + + Q+ Sbjct: 425 SIRRMDRALREFRIRGVASNLQFLENVINHPAFRSGDVTTRFI-DKTPELLAFTKRQD 481 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: 1200 Number of extensions: 50 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 509 Length of database: 1167 Length adjustment: 41 Effective length of query: 468 Effective length of database: 1126 Effective search space: 526968 Effective search space used: 526968 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: 55 (25.8 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