GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Escherichia coli BW25113

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate 14644 b0507 glyoxylate carboligase (NCBI)

Query= BRENDA::P9WG41
         (618 letters)



>FitnessBrowser__Keio:14644
          Length = 593

 Score =  344 bits (882), Expect = 7e-99
 Identities = 203/557 (36%), Positives = 292/557 (52%), Gaps = 12/557 (2%)

Query: 35  LQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASG 94
           + ++    A +  LE+ G+   FG+PG A+ P Y  +     +RH+L RH +GA H A G
Sbjct: 1   MAKMRAVDAAMYVLEKEGITTAFGVPGAAINPFYSAMRKHGGIRHILARHVEGASHMAEG 60

Query: 95  YAHVT-GRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADIS 153
           Y   T G +GVC+ TSGP  T+++T L  A  DSIP++ ITGQ  R  +  + FQ  DI 
Sbjct: 61  YTRATAGNIGVCLGTSGPAGTDMITALYSASADSIPILCITGQAPRARLHKEDFQAVDIE 120

Query: 154 GITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME 213
            I  P++K    VR    +PRVL +AFH+  SGRPG VLVD+P DV   +  F       
Sbjct: 121 AIAKPVSKMAVTVREAALVPRVLQQAFHLMRSGRPGPVLVDLPFDVQVAEIEFDPDMYEP 180

Query: 214 LPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTL 273
           LP YKP       Q+ +A +++  A +PV+  GGGVI  +A   L++ AELT +PV+ TL
Sbjct: 181 LPVYKPAAS--RMQIEKAVEMLIQAERPVIVAGGGVINADAAALLQQFAELTSVPVIPTL 238

Query: 274 MARGAFPDSHRQNLGMPGMHGTVA-AVAALQRSDLLIALGTRFDDRVTGKLDSFAPEAKV 332
           M  G  PD H    GM G+        A L  SD++  +G RF +R TG ++ +    K+
Sbjct: 239 MGWGCIPDDHELMAGMVGLQTAHRYGNATLLASDMVFGIGNRFANRHTGSVEKYTEGRKI 298

Query: 333 IHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTY 392
           +H DI+P +IG+    D+ IV D KA +T L+ + +     G +     W      RK  
Sbjct: 299 VHIDIEPTQIGRVLCPDLGIVSDAKAALTLLVEVAQEMQKAGRLPCRKEWVADCQQRKRT 358

Query: 393 PLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNSGGL 452
            L      +  + P+ V E++ +  G D  +V  +G  Q+ AAQ +   K R W+N G  
Sbjct: 359 LLRKTHFDNVPVKPQRVYEEMNKAFGRDVCYVTTIGLSQIAAAQMLHVFKDRHWINCGQA 418

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

Query: 513 VRQWQSLFYAERYSQTDLAT-HSHRI----PDFVKLAEALGCVGLRCEREEDVVDVINQA 567
           +RQ Q  F  +   Q      +S  +     D VK+AE LGC  +R  + ED+     QA
Sbjct: 479 IRQSQRAFDMDYCVQLAFENINSSEVNGYGVDHVKVAEGLGCKAIRVFKPEDIAPAFEQA 538

Query: 568 RAI---NDCPVVIDFIV 581
           +A+      PVV++ I+
Sbjct: 539 KALMAQYRVPVVVEVIL 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: 899
Number of extensions: 57
Number of successful extensions: 6
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: 593
Length adjustment: 37
Effective length of query: 581
Effective length of database: 556
Effective search space:   323036
Effective search space used:   323036
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.

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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