GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Rhodobacter viridis JA737

Align bifunctional L-rhamnulose 1-phosphate aldolase/lactaldehyde dehydrogenase (EC 4.1.2.19; EC 1.2.1.22) (characterized)
to candidate WP_110805876.1 C8J30_RS10870 bifunctional aldolase/short-chain dehydrogenase

Query= metacyc::BSU31220-MONOMER
         (689 letters)



>NCBI__GCF_003217355.1:WP_110805876.1
          Length = 677

 Score =  309 bits (791), Expect = 3e-88
 Identities = 222/696 (31%), Positives = 342/696 (49%), Gaps = 40/696 (5%)

Query: 1   MVKHIWDSERAAQLPKGVEELVYRSNLIGSDRTVCNWGGGNTSMKTTEKDFRGREIEVMW 60
           M++++W  E AA     + + +Y S LIGSD  +   GGGNTS+KT   D  G  + V+ 
Sbjct: 1   MIRNLWSDEAAAAAGGDLGQRIYTSRLIGSDPELVLHGGGNTSVKTEAVDLFGETVSVLH 60

Query: 61  VKGSGSDLATMKAHNFSGLKLDDIRPLIKRDQMPDEEMVDYLSHCMIDSKHPRPSIETLL 120
           VKGSG DLAT+ A     ++LD +  L   D +PD+ +V      ++D   P PS+E LL
Sbjct: 61  VKGSGHDLATIDAAGMPAVRLDPMLRLKDFDAVPDDVLVKLQRLNLLDPAAPNPSVEMLL 120

Query: 121 HAFLPYKHVDHTHPDAIISICCADNGKQIAEDIYGNRFVWVPYVRPGFTLSKMIAEGVAN 180
           H FLP+K VDHTH    + +      +    +++G+R   VP+V+PGF L+K      A 
Sbjct: 121 HVFLPHKFVDHTHATPFLVLANLPEAEAAIRELFGDRMALVPFVKPGFGLAKAGLATYAA 180

Query: 181 NPHAELVLMEKHGLVTWGETSETCYQKTISIIQEAEQYINDRINQHEVFGGKRYQPLPED 240
           +P  E +L++ HG  TWG  +++ Y K I+     E ++ DR     +        LP  
Sbjct: 181 HPGVEALLLKNHGHFTWGPDAKSSYFKVIAHANLVEAWLADRRPAPLLPAA----ALPVA 236

Query: 241 KRKQILAGIMPVIRGAVSEEKKM-ILSYDDHDDVLEFVNSVQAPALSQIGAACPDHLVHT 299
           +   +LA +   +  A+ EE  + +L     D    FV+     AL++ G   PDH++ T
Sbjct: 237 EVAPVLAALRGALASALPEEAALPVLDLRADDATRAFVSRPDLEALAKAGVVTPDHVIRT 296

Query: 300 KRVPLYIDWNPETQDVHKLADLIKSGVETFTSEYQAYFTRNQ-QDGDQI--FESAPRVIL 356
           K   L +      +   +  + +++ V  + S Y+AYF  N+ + G  +      P +I 
Sbjct: 297 KGEVLVL------RQAAQRPEAMRAAVTDYVSRYRAYFEANKARFGGPVAMLNPMPGLIW 350

Query: 357 IPGIGMVNTGKSYAMSKVSGALYRRAIAVMKGATALGQFVSLHENESYHVEYWPLELYKL 416
           + GIG V  G     ++++  +  ++  V     A G F S+ + + + +EYWPLEL KL
Sbjct: 351 LEGIGAVGAGADAKAARIAADIGDQSARVKADGLAAGGFRSIADADLFDMEYWPLELAKL 410

Query: 417 TLAPPEAEFSRKVALITGGAGGIGSAACRRFAAEGGHVIVADLNIEGAQK-IAGEINDAY 475
             A   A    +V L+TGGAG IG A    FAA+G  + + D   E  +K +AG   DA 
Sbjct: 411 GTAKAPA-LQGRVVLVTGGAGAIGLATAEAFAAQGASIFLVDRPGEVLEKAVAGLGRDAA 469

Query: 476 GKGRAMAVKMDVTKEEDVQSAFERAALAYGGIDIVVNNAGLATS---SPFDETSLKEWNL 532
           G G       D+T+     +A    A  +GG+DI+V+NAG A +   +  DE  L+  + 
Sbjct: 470 GHG------CDITQPGAAAAAVAACAARFGGLDILVSNAGAAITGDIATLDEQVLR-GSF 522

Query: 533 NMNVLGTGYFLVAREAFKQMKHQNRG------GSMVFVGSKNSVYAGKNASAYSSVKALE 586
            +N      F  A  A  + +   RG      G ++F  SK +V  GK  +AY   KA  
Sbjct: 523 ELNFFSHLAFSQAAIALYRAQAAGRGTRGAEPGQILFNVSKQAVNPGKGFAAYGLPKATS 582

Query: 587 THLARCIAAEGGEFGIRVNSVLPDAVLQGSAIWGSSWREERAAAYGIEPDQLEEHYRKRT 646
             L R +A E G  GIRVN +  D +  G  +        R++A GI+       Y    
Sbjct: 583 FFLLRQLALELGPEGIRVNGINADRIRSG--LLTPEMIAARSSARGIDAGT----YMAGN 636

Query: 647 ALLVNIYPEDIAEAIAFFASSKAEKTTGCMITVDGG 682
            L V +    +AE  AF A ++AE+TT  ++TVDGG
Sbjct: 637 LLKVEVEARHVAE--AFVALARAERTTAHVMTVDGG 670


Lambda     K      H
   0.317    0.134    0.396 

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: 978
Number of extensions: 47
Number of successful extensions: 8
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: 689
Length of database: 677
Length adjustment: 39
Effective length of query: 650
Effective length of database: 638
Effective search space:   414700
Effective search space used:   414700
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: 54 (25.4 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