GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Azohydromonas australica DSM 1124

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_029001697.1 H537_RS0135675 glyoxylate carboligase

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000430725.1:WP_029001697.1
          Length = 598

 Score =  331 bits (848), Expect = 6e-95
 Identities = 194/563 (34%), Positives = 289/563 (51%), Gaps = 20/563 (3%)

Query: 35  LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94
           + ++  A A +  +E+ GV   FG+PG A+ P+Y  L +   + HVL RH + A H A G
Sbjct: 1   MAKMKAAMAAVLVMEKEGVSQAFGVPGAAINPLYAALRERGGISHVLARHVEAASHMAEG 60

Query: 95  YAHV-TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153
           Y     G +GVC+ TSGP  T+++T L  A  DSIP++ ITGQ  R  +  + FQ  DI 
Sbjct: 61  YTRARAGNIGVCIGTSGPAGTDMITGLYSAGADSIPILCITGQAPRARLYKEDFQAVDIE 120

Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213
            I  P+TK    VR    +PR   +AFH+  SGRPG VL+D+P DV   +  F       
Sbjct: 121 SIAKPVTKWAVTVREPAQVPRAFQQAFHLMRSGRPGPVLIDLPFDVQMAEIEFDIDTYEP 180

Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273
           LP YKP      +Q+ +A  ++ A+ KP++  GGG+I  +A+  L ELAE  G+PV+ TL
Sbjct: 181 LPVYKPAAS--RKQIDKALDMLLASEKPLIVAGGGIINADASNLLVELAETLGVPVIPTL 238

Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332
           M  G+ PD H    GM G+  +     A +  SD ++ +G R+ +R TG +D +      
Sbjct: 239 MGWGSIPDDHPLMAGMVGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSVDVYTKGRTF 298

Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392
           +H DI+P +IG+    D  IV D KA +   +   +     GT++  D WA+    RK  
Sbjct: 299 VHVDIEPTQIGRVFMPDFGIVSDAKAALELFVQAAKERKAAGTLKSYDDWAFRCAERKRL 358

Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452
                      + P  V E++  +   D ++V+ +G  Q+  AQF+    PR W+N G  
Sbjct: 359 MHRKSHYEQTPIKPMRVYEEMNAVFPRDTIYVSTIGLSQIAGAQFLHVYGPRQWINCGQA 418

Query: 453 GTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGNLGM 512
           G +G+ IPAA+G   A P   V  + GD  FQ   +ELA  A   +P    L+NN  LG+
Sbjct: 419 GPLGWTIPAALGVVAADPTRTVVGLSGDYDFQFLIEELAVGAQFRLPYVQVLVNNSYLGL 478

Query: 513 VRQWQSLFYAERYSQTDLATHSHRIP-----------DFVKLAEALGCVGLRCEREEDVV 561
           +RQ Q  F  +   Q  L+  +  +P           D V + E LGC  LR    E + 
Sbjct: 479 IRQAQRGFDMDYCVQ--LSFENQNMPEEAGELRGYGVDHVTVVEGLGCKALRVTDPEKIG 536

Query: 562 DVINQARAI---NDCPVVIDFIV 581
           + + QA A+   +  PVV++ I+
Sbjct: 537 ETLKQAHAMALEHRVPVVVECIL 559


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: 956
Number of extensions: 59
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: 598
Length adjustment: 37
Effective length of query: 581
Effective length of database: 561
Effective search space:   325941
Effective search space used:   325941
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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