GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= metacyc::MONOMER-11560
         (497 letters)



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

 Score =  760 bits (1963), Expect = 0.0
 Identities = 364/496 (73%), Positives = 425/496 (85%)

Query: 2   TTLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANR 61
           T  TR+DWE  A  L I G+AFINGEY DA SG TF+C+SP+DGR LA VASCDL DAN 
Sbjct: 3   TPKTRSDWENLAVSLAINGKAFINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANI 62

Query: 62  AVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDI 121
           AV NAR  F+SGVWS+ AP KRK  +IRFA+LL +N  ELALLETLDMGKPI  S ++D+
Sbjct: 63  AVANAREVFDSGVWSKAAPVKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDV 122

Query: 122 PGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPA 181
            GAA+AI W+ EAIDK+YDE+APT H+++G++TREPVGVV AIVPWNFPLLMACWKLGPA
Sbjct: 123 AGAARAIRWSGEAIDKLYDELAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPA 182

Query: 182 LATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLV 241
           L TGNSV+LKPSEKSPLTAIRIA+LA++AGIP GVLNVLPGYGHTVGKALALHMDVDTLV
Sbjct: 183 LVTGNSVILKPSEKSPLTAIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLV 242

Query: 242 FTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301
           FTGSTKIAKQLM+YAGESNMKR+WLEAGGKSPNIVF DAPDL+AAA AAA AI FNQGEV
Sbjct: 243 FTGSTKIAKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEV 302

Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361
           CTAGSRLLVE  +KD+ + ++ E L  W+PG+PL+P T  GA+VD QQ++T+LSYI+AG 
Sbjct: 303 CTAGSRLLVESGVKDELVGLIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQ 362

Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421
            +GA L+ GG++ L ETGG YV+PT+F  V N M+IA EEIFGPVLSVI F+  EEA+AI
Sbjct: 363 NEGASLVYGGQQVLAETGGVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAI 422

Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSL 481
           ANDT YGLAAG+WT+DISKAHKTA+A+R+G VW+N YDGGDMTAPFGG+KQSGNGRDKSL
Sbjct: 423 ANDTIYGLAAGVWTADISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSL 482

Query: 482 HALEKYTELKATWIKL 497
           H+ +KYTE+KATWI L
Sbjct: 483 HSFDKYTEIKATWIVL 498


Lambda     K      H
   0.316    0.132    0.390 

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: 849
Number of extensions: 33
Number of successful extensions: 2
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: 497
Length of database: 498
Length adjustment: 34
Effective length of query: 463
Effective length of database: 464
Effective search space:   214832
Effective search space used:   214832
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 (21.6 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