GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Marinobacter adhaerens HP15

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Marino:GFF3684
          Length = 489

 Score =  286 bits (733), Expect = 8e-82
 Identities = 172/474 (36%), Positives = 263/474 (55%), Gaps = 10/474 (2%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           ++ G+F+         VVNPAT  VI  +        + AI++A     EW A+ AIER+
Sbjct: 11  FVHGRFLANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIERS 70

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAE-VEVAFTADYIDYMAEWARRYEGEIIQ 128
             L +  A +RER  E++A  V + GK  Q AE V+V   AD +++ A  A   EG   Q
Sbjct: 71  RILLRAVAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGN--Q 128

Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188
            D  G+     +  LG+  GI  WN+P  +   K APAL  GN ++ KPSE TP  A+  
Sbjct: 129 QDLGGDFYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKL 188

Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
           A+I  E G+P GVFN+V G  E VGQ L  +P++A VS TG V+ G+K+MA A+  +  V
Sbjct: 189 AEIFTEAGVPAGVFNVVQGAAE-VGQWLTHHPEIAKVSFTGEVATGKKVMAAASSTLKDV 247

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGE- 307
            +ELGGK+P I+ DDADLE A+ A +       G++C    RV+V + +Y +F+ RL E 
Sbjct: 248 TMELGGKSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLER 307

Query: 308 AMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGK----GY 363
               ++ G+P    D   G LI+A   + V   +A+ + EGA ++ GG+A E +    GY
Sbjct: 308 TRNNIKPGDPM-NPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKGGY 366

Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423
           +  PT+  D   +M+I+ EE FGPV+ V+ F   ++ I+ AN++D GL + ++T ++  A
Sbjct: 367 FVEPTIFTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRA 426

Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
            + I  ++ G  +IN       +    G++ SGIG  +G+  +  Y Q + VY+
Sbjct: 427 HRVIHQIQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYV 480


Lambda     K      H
   0.318    0.135    0.392 

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: 574
Number of extensions: 24
Number of successful extensions: 4
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: 479
Length of database: 489
Length adjustment: 34
Effective length of query: 445
Effective length of database: 455
Effective search space:   202475
Effective search space used:   202475
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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