Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS07965 AZOBR_RS07965 glyoxylate carboligase
Query= BRENDA::P9WG41 (618 letters) >FitnessBrowser__azobra:AZOBR_RS07965 Length = 589 Score = 337 bits (864), Expect = 9e-97 Identities = 198/561 (35%), Positives = 297/561 (52%), Gaps = 20/561 (3%) Query: 35 LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94 + ++ +A + LE+ GV V FG+PG A+ P Y L + ++ HVL RH +GA H A G Sbjct: 1 MARMMAIEAAVHVLEKEGVSVCFGVPGAAINPFYAALQRNGRIGHVLARHVEGASHMAEG 60 Query: 95 YAHV-TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153 Y G +GVC+ TSGP T+++T L A DSIP++ ITGQ R + + FQ DI Sbjct: 61 YTRAKAGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLHKEDFQAVDIP 120 Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213 I P+ K V +P +AFH+ SGRPG VL+D+P DV + F Sbjct: 121 SIAKPVAKWAVTVLEPGQVPYAFQQAFHLMRSGRPGPVLLDLPIDVQMAEIEFDPDAYEP 180 Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273 LP YKP QV +A ++ AA +P+L GGG+I +A+++L E AE+ G+PV+ TL Sbjct: 181 LPTYKPAAT--RAQVEKALAMLNAAERPLLVAGGGIINADASDRLVEFAEIAGLPVIPTL 238 Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332 MA GA PD H GM G+ AA+ SD ++ +G R+ +R TG +D + K Sbjct: 239 MAWGAIPDDHPLMAGMVGLQTAHRYGNAAMLASDFVLGIGNRWANRHTGSVDVYTKGRKF 298 Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADW--WAYLNGVRK 390 +H DI+P +IG+ D+ IV D A + I + + G ++ DW W VRK Sbjct: 299 VHVDIEPTQIGRVFAPDLGIVSDAGAALDLFIEVAKEWKAAG--KLRDWSEWVKTCQVRK 356 Query: 391 TYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSG 450 L ++ + P+ V +++ G D +V+ +G Q+ AQF+ KPR W+N G Sbjct: 357 RSMLRRSDFANVPIKPQRVYQEMNSAFGEDVCYVSTIGLSQIAGAQFLHVYKPRHWINCG 416 Query: 451 GLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNL 510 G +G+ +PAA+G ++A P ++ A+ GD FQ +ELA A +P L+NN L Sbjct: 417 QAGPLGWTLPAALGVRVADPKRKIVALSGDYDFQFLIEELAVGAQFKLPYIHVLVNNSYL 476 Query: 511 GMVRQWQSLFYAERYSQTDLATHSHRIP-------DFVKLAEALGCVGLRCEREEDVVDV 563 G++RQ Q F + Q L+ + P D V +AE LGC +R +++ Sbjct: 477 GLIRQAQRAFQMD--FQVQLSFENINAPEIGVYGVDHVAVAEGLGCKAIRVTDPDNLQSA 534 Query: 564 INQARAIND---CPVVIDFIV 581 QA+ D PVV++ I+ Sbjct: 535 FAQAQQWMDEFQVPVVVEVIL 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: 980 Number of extensions: 62 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: 618 Length of database: 589 Length adjustment: 37 Effective length of query: 581 Effective length of database: 552 Effective search space: 320712 Effective search space used: 320712 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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