GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Marinobacter adhaerens HP15

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase

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



>FitnessBrowser__Marino:GFF3202
          Length = 533

 Score =  348 bits (893), Expect = e-100
 Identities = 192/476 (40%), Positives = 279/476 (58%), Gaps = 12/476 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           +I GE+   V G+ FE ++PV G  + ++      D + A++ A     +  W + +P +
Sbjct: 49  YIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKA--APAWGKTSPTE 106

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L++ AD +  N+E+LA+ ET D GK + ++ + DIP AA    + A  +      +
Sbjct: 107 RSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGHM 166

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
               H+ +     EP+GVVG I+PWNFP+LMA WKLGP LA GN  VLKP+E++P + + 
Sbjct: 167 GEIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASILV 226

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + ++ I   +P GVLN++ GYG   G+ALA    +  + FTGST +   ++  A E N+ 
Sbjct: 227 LMEI-IGDLLPPGVLNIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHILKCAAE-NII 284

Query: 263 RIWLEAGGKSPNIVFADA----PDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
              +E GGKSPNI F+D     P+             FNQGEVCT  SR LV+  + ++F
Sbjct: 285 PSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLAFFNQGEVCTCPSRALVQEDMFEEF 344

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT-LEE 377
           +  VV+  K  K GNPLD    VGA    +Q + ++SY+  G ++GA +L GG R  L+E
Sbjct: 345 MQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHLDE 404

Query: 378 --TGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
               G Y++PT+F G  N MR+ QEEIFGPV+ V  F T EEA+AIANDT +GL AG+WT
Sbjct: 405 EFNNGFYIQPTLFKG-DNKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAGVWT 463

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            D + A++  R ++AG VW+N Y      A FGG+K+SG GR+    ALE Y + K
Sbjct: 464 RDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTK 519


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: 674
Number of extensions: 34
Number of successful extensions: 7
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: 533
Length adjustment: 35
Effective length of query: 462
Effective length of database: 498
Effective search space:   230076
Effective search space used:   230076
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