GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF in Shewanella oneidensis MR-1

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= SwissProt::P42236
         (488 letters)



>lcl|FitnessBrowser__MR1:202599 SO3496 aldehyde dehydrogenase (NCBI
           ptt file)
          Length = 498

 Score =  290 bits (742), Expect = 8e-83
 Identities = 175/480 (36%), Positives = 273/480 (56%), Gaps = 13/480 (2%)

Query: 13  FINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA--KTAWRKLTGA 70
           FINGE+  + SG+     +P D   ++  V +    D   AV  A E      W K    
Sbjct: 24  FINGEYRDASSGNTFDCISPID-GRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAPV 82

Query: 71  ERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDV 130
           +R Q + + A+++E+   E+A   T +MGK +  +K     G A    ++GE + K  D 
Sbjct: 83  KRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYDE 142

Query: 131 IPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCA 190
           +  T  + +   TR P+GVV  I PWNFP+ +  WK+ PALV GN+V++KP+ ++ +T  
Sbjct: 143 LAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLTAI 202

Query: 191 KIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGK-IIGQAALARG 249
           +I     +AG+P GV+N++ G G  VG+ LA H  V+ + FTGS ++ K ++  A  +  
Sbjct: 203 RIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNM 262

Query: 250 AKYQLEMGGKNPVIVADDA-DLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEK 308
            +  LE GGK+P IV +DA DL+AAA A       + G+ CTA SR++V+SG+ +     
Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELVGL 322

Query: 309 LLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKL--ENGKY 366
           + +       G  L+     G +  K QLD  LSYI+ G+ EGASL+ GG+++  E G  
Sbjct: 323 IAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAETG-- 380

Query: 367 QNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTEN 426
             G YVQP +F NV ++M IA EEIFGPV+++I+ + +EEA+ IAND  +GL+A ++T +
Sbjct: 381 --GVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTAD 438

Query: 427 IGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFV 486
           I +       + +G+V IN    G ++ APFGG KQ S + R++   + D +T IK  ++
Sbjct: 439 ISKAHKTAKALRSGMVWINHYDGG-DMTAPFGGYKQ-SGNGRDKSLHSFDKYTEIKATWI 496


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: 581
Number of extensions: 27
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: 488
Length of database: 498
Length adjustment: 34
Effective length of query: 454
Effective length of database: 464
Effective search space:   210656
Effective search space used:   210656
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, the preprint on GapMind for carbon sources, 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