Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate PP_4297 PP_4297 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__Putida:PP_4297 Length = 591 Score = 326 bits (835), Expect = 2e-93 Identities = 194/560 (34%), Positives = 291/560 (51%), Gaps = 18/560 (3%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + ++ A + + GVD FGIPG A+ P+Y L + HVL RH +GA H A G Sbjct: 1 MSKMRAIDAAVLVMRREGVDTAFGIPGAAINPLYSALKKVGGIDHVLARHVEGASHMAEG 60 Query: 95 YAHVT-GRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 Y G +GVC+ TSGP T++VT L A DSIP++ ITGQ R + + FQ DI+ Sbjct: 61 YTRANPGNIGVCIGTSGPAGTDMVTGLYSASADSIPILCITGQAPRARLHKEDFQAVDIT 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+TK V +P +AF+ +GRPG VL+D+P DV + F Sbjct: 121 NIVKPVTKWATTVLEPGQVPYAFQKAFYEMRTGRPGPVLIDLPFDVQMAEIEFDIDAYEP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 LP +KP+ Q +A L+ A +P+L GGG+I +A+++L E AELTG+PV+ TL Sbjct: 181 LPVHKPSAT--RVQAEKALALLNDAERPLLVAGGGIINADASDKLVEFAELTGVPVIPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 M G PD H Q +GM G+ + A L +SDL+ +G R+ +R TG +D + K Sbjct: 239 MGWGTIPDDHAQMVGMVGLQTSHRYGNATLLKSDLVFGIGNRWANRHTGSVDVYTEGRKF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392 +H DI+P +IG+ D+ IV D + + + R G ++ W RK+ Sbjct: 299 VHVDIEPTQIGRVFTPDLGIVSDAGKALDVFLEVAREWKAAGKLKCRKAWLEECQERKSS 358 Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452 + + P+ V E++ ++ G D +V+ +G Q+ AQF+ KPR W+N G Sbjct: 359 LQRKTHFDNVPVKPQRVYEEMNQVFGKDTCYVSTIGLSQIAGAQFLHVYKPRHWINCGQA 418 Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512 G +G+ IPAA+G A P +V A+ GD FQ +ELA A +P L+NN LG+ Sbjct: 419 GPLGWTIPAALGVVKADPKRKVVALSGDYDFQFMIEELAVGAQFNLPYVHVLVNNAYLGL 478 Query: 513 VRQWQSLF--------YAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVI 564 +RQ Q F E + TD AT+ D V + E LGC +R ++ + Sbjct: 479 IRQAQRGFDMDYCVQLAFENINSTDAATYG---VDHVAVVEGLGCKAIRVFEPAEIAPAL 535 Query: 565 NQARAIND---CPVVIDFIV 581 +A+ + + PVV++ I+ Sbjct: 536 IKAQKMAEEFRVPVVVEVIL 555 Lambda K H 0.319 0.136 0.414 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: 958 Number of extensions: 54 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: 618 Length of database: 591 Length adjustment: 37 Effective length of query: 581 Effective length of database: 554 Effective search space: 321874 Effective search space used: 321874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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