GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Shewanella loihica PV-4

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

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



>lcl|FitnessBrowser__PV4:5208455 Shew_0967 aldehyde dehydrogenase
           (RefSeq)
          Length = 498

 Score =  745 bits (1924), Expect = 0.0
 Identities = 361/496 (72%), Positives = 417/496 (84%)

Query: 2   TTLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANR 61
           T   R  W++ A  L I+G+AFINGEY  A S +TF+C+SP+DGR L +VASCDL DANR
Sbjct: 3   TPQNREQWQEMADSLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANR 62

Query: 62  AVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDI 121
           AV NAR  F  G WSQL P KRK  +IRFADLL  N +ELALLETLDMGKPI  S ++D+
Sbjct: 63  AVANAREVFERGDWSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDV 122

Query: 122 PGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPA 181
            GAA+A+ W+ EA+DK+YDE+APT H+++G++TREPVGVV AIVPWNFPLLMACWKLGPA
Sbjct: 123 AGAARALRWSGEAVDKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPA 182

Query: 182 LATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLV 241
           LATGNSVVLKPSEKSPLTAIR+AQLAIEAGIP GVLNVLPGYGHTVGKALALHMDVDTLV
Sbjct: 183 LATGNSVVLKPSEKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLV 242

Query: 242 FTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301
           FTGSTKIAKQLM+YAGESNMKR+WLEAGGKSPNIVF DAP+L+ AA AAASAIAFNQGEV
Sbjct: 243 FTGSTKIAKQLMIYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEV 302

Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361
           CTAGSRLLVE  +K++ + ++   ++ W+PG+PLDP TT GA+VD QQ+  VL YI AG 
Sbjct: 303 CTAGSRLLVESGVKEELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGV 362

Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421
            +GA+L  GG++ L ETGG YV PTIF  V N M IA+EEIFGPVLSVI FD  EEA+ I
Sbjct: 363 AEGAQLRQGGQQVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRI 422

Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSL 481
            NDT YGLAAG+WTSDISKAHKTA+A+R+G VW+N YDGGDMTAPFGG+KQSGNGRDKSL
Sbjct: 423 GNDTIYGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSL 482

Query: 482 HALEKYTELKATWIKL 497
           HA +KYTE+KATWI L
Sbjct: 483 HAFDKYTEIKATWIAL 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: 815
Number of extensions: 27
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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