GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Erythrobacter gangjinensis K7-2

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate WP_047006047.1 AAW01_RS04300 aldehyde dehydrogenase family protein

Query= SwissProt::Q1JUP4
         (481 letters)



>NCBI__GCF_001010925.1:WP_047006047.1
          Length = 479

 Score =  233 bits (593), Expect = 1e-65
 Identities = 147/458 (32%), Positives = 232/458 (50%), Gaps = 11/458 (2%)

Query: 26  IDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATMRKAAALVRERA 85
           ++V++  TG+   RVA A    +D+A+A A +      ++ ++ER A +    +  RER 
Sbjct: 25  LEVIDKYTGEVAFRVAQADPEIIDKAIAGAVAATGPMARLASYERKAVLEHCVSRFRERF 84

Query: 86  DAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP----PRNLGAQQTVV 141
           D +A  +  E GKP+ ++  EV    D     A+E  R+YG ++P     R  G Q    
Sbjct: 85  DELAYALCVEAGKPIGDSEGEVTRLIDTFVIAAEESTRMYGEVMPLDISERAKGYQSIWK 144

Query: 142 KEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVPA 201
           + PVGP +  +P+NFP+N    K++ A+A GC F++K   +TP     +     +  +P 
Sbjct: 145 RYPVGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASKTPLGAIIIGEILAETDLPE 204

Query: 202 GVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPVI 261
           G   ++     + +        ++ ++FTGS  VG  L + +G   K+  +ELGG+A VI
Sbjct: 205 GAFSILPAS-RDGADLFTEDERLKLLSFTGSPAVGWALKAKSG--KKKVVLELGGNAAVI 261

Query: 262 VAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGLE 321
           V  DAD+  A++      F  +GQ CI   R L+H  + D F   LV+  + LK G+  +
Sbjct: 262 VDRDADLEDALERIVFGAFYQSGQSCIGVQRILIHEEVYDRFKEMLVEKTKTLKAGDPKD 321

Query: 322 EGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADVF 381
             T +G + +      +   ID A   GA++  GG   G +GN    T++  V   A V 
Sbjct: 322 RDTFIGPMIDEGEAQRLKGWIDEAVGHGATLLCGG---GCKGNMLEATLLEGVDKHAKVL 378

Query: 382 NNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQ- 440
           N E FGP+A ++ F  ++EA+ E NR  FGL    FTR    +     RLEVG + IN  
Sbjct: 379 NEEAFGPLAILQPFATMDEALEEVNRSEFGLQAGIFTRDLFAMFDAWDRLEVGGIVINDV 438

Query: 441 PATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478
           P+     MP+GGVKDSG G EG   A+E     +++ +
Sbjct: 439 PSYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVI 476


Lambda     K      H
   0.318    0.134    0.393 

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: 575
Number of extensions: 32
Number of successful extensions: 5
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: 481
Length of database: 479
Length adjustment: 34
Effective length of query: 447
Effective length of database: 445
Effective search space:   198915
Effective search space used:   198915
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 24 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