GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Algoriphagus aquaeductus T4

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_111391131.1 CLV31_RS01670 SDR family oxidoreductase

Query= reanno::ANA3:7024897
         (256 letters)



>NCBI__GCF_003253485.1:WP_111391131.1
          Length = 256

 Score =  107 bits (268), Expect = 2e-28
 Identities = 76/252 (30%), Positives = 121/252 (48%), Gaps = 13/252 (5%)

Query: 10  LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69
           LQ K I ISGGA GIG  +    +E+GA    +D   +E  +LV              + 
Sbjct: 5   LQDKVILISGGAKGIGGAISKGLIEEGAIPVIIDPSEKEGKELVELAVGKALHLPWRLFS 64

Query: 70  CDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFA 129
            +  + A L+ V A      G I  ++NNA  +    +++ +PE + Q +  NL HY+  
Sbjct: 65  AEDCEKAVLEAVRA-----FGRIDGVVNNAGANDGVGLEKGSPEAFAQSIANNLHHYYSL 119

Query: 130 VQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRIN 189
           V    P++++   G+++N+ S +    Q G +GY A+K   + LTR  + +L    IR+N
Sbjct: 120 VHFALPELKK-SQGAIVNISSKTAVTGQGGTSGYVAAKGAQLALTREWSVELLPYHIRVN 178

Query: 190 TLTPGWVMTKRQLTHWVD---KDTAKHIENNQCI---KEYVMPEDIAAMALFLAADDSKL 243
            + P  V T      W+        K  E N  I   K    PE+IA+MA+FL ++ +  
Sbjct: 179 AILPAEVYTP-MYESWIQTFPNPEEKLAEINHQIPLGKRMTTPEEIASMAIFLLSNRASH 237

Query: 244 CTAQNFIVDGGW 255
            T Q+  VDGG+
Sbjct: 238 ITGQHLYVDGGY 249


Lambda     K      H
   0.320    0.134    0.406 

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: 166
Number of extensions: 11
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: 256
Length of database: 256
Length adjustment: 24
Effective length of query: 232
Effective length of database: 232
Effective search space:    53824
Effective search space used:    53824
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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