GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sphingomonas koreensis DSMZ 15582

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Korea:Ga0059261_3374
          Length = 474

 Score =  266 bits (681), Expect = 9e-76
 Identities = 168/471 (35%), Positives = 264/471 (56%), Gaps = 14/471 (2%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI G++V   G    DV+NPATEA ++ I  G   DA KA+ AA+ A   +      ER 
Sbjct: 8   YIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDERI 67

Query: 70  SWLRKISAGIRERASEIS-ALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
           + L  I A  + RA +++ A+  E G  I      +V     ++       + +E     
Sbjct: 68  ALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKAFEF---- 123

Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188
           S++ G+++++ +  +GV   I PWN+P   I  K+APAL  GNT+V+KPSE  P +A  F
Sbjct: 124 SEQIGQSLVVHE-PIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182

Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
           A+I+D+ G+P GVFNLV G G  VG  L+ +  V MVS TGS  AG ++   AA+ + +V
Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETVKRV 242

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
             ELGGK+P +++  ADL  AV+  + S V+NSGQ C    R+ V +    +        
Sbjct: 243 HQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIASGL 302

Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGG----KAVEGKGYY 364
           M+AV+ G+PA+     +GP++N A  E+++  + + +EEGA++  GG      +E  GY+
Sbjct: 303 MKAVETGDPAQEGR-HIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDGIE-TGYF 360

Query: 365 YPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAM 424
             PTL   VR +M+I  EE FGPV+ ++ +   E+A+ +AND+DYGL++ ++     V  
Sbjct: 361 VKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVLFGSPEEVKR 420

Query: 425 KAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
            A + L+ G  YIN    +    F  G+++SG G   GK GL E+++ + +
Sbjct: 421 VAPR-LRAGMVYINGGQPDPSLPF-GGYKQSGNGREHGKFGLAEFMEVKAM 469


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: 513
Number of extensions: 26
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: 474
Length adjustment: 33
Effective length of query: 446
Effective length of database: 441
Effective search space:   196686
Effective search space used:   196686
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: 51 (24.3 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