GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5208455
          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:

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