GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Escherichia coli BW25113

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)

Query= SwissProt::P42236
         (488 letters)



>lcl|FitnessBrowser__Keio:14450 b0312 betaine aldehyde
           dehydrogenase, NAD-dependent (NCBI)
          Length = 490

 Score =  319 bits (818), Expect = 1e-91
 Identities = 183/489 (37%), Positives = 276/489 (56%), Gaps = 9/489 (1%)

Query: 1   MSVITEQNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA 60
           MS + EQ  Y   I+G +  + SG   +  NPA+ N ++  VQ +  EDV+RAV +A + 
Sbjct: 1   MSRMAEQQLY---IHGGYTSATSGRTFETINPANGN-VLATVQAAGREDVDRAVKSAQQG 56

Query: 61  KTAWRKLTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYY 119
           +  W  +T  ER + L +  DI+ +R +E+A   T + GK   E    +   G  +L YY
Sbjct: 57  QKIWASMTAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYY 116

Query: 120 AGEGMRKTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVI 179
           AG      G  IP  +  + ++T R PLGVV  I  WN+P+ I +WK APAL  GN ++ 
Sbjct: 117 AGLIPALEGSQIPLRET-SFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIF 175

Query: 180 KPATETAVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGK 239
           KP+  T +T  K+   + EAGLP GV N++ G G+  GQ L EH G+  V+FTG    GK
Sbjct: 176 KPSEVTPLTALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGK 235

Query: 240 -IIGQAALARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQ 298
            ++  +A +   +  +E+GGK+P+IV DDADL+ AA+  +   F S+GQ CT  +RV V 
Sbjct: 236 KVMANSAASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVP 295

Query: 299 SGIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGG 358
           +     F++K+L R + I  GD        GP+ S    DN L YI KGK+EGA +L GG
Sbjct: 296 AKCKAAFEQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGG 355

Query: 359 EKLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418
           + L+   + NG +V P +F + + +MTI +EEIFGPV++++  +S +E +  AND  +GL
Sbjct: 356 DVLKGDGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGL 415

Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478
           +A I T ++ R    I +++AG+  IN        + P GG K S    RE G      +
Sbjct: 416 AAGIVTADLNRAHRVIHQLEAGICWINTWGES-PAEMPVGGYKHSGI-GRENGVMTLQSY 473

Query: 479 TAIKTVFVK 487
           T +K++ V+
Sbjct: 474 TQVKSIQVE 482


Lambda     K      H
   0.315    0.132    0.374 

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: 570
Number of extensions: 31
Number of successful extensions: 3
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: 488
Length of database: 490
Length adjustment: 34
Effective length of query: 454
Effective length of database: 456
Effective search space:   207024
Effective search space used:   207024
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 (21.5 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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