GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Streptacidiphilus oryzae TH49

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_037570579.1 BS73_RS07645 glucose 1-dehydrogenase

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



>NCBI__GCF_000744815.1:WP_037570579.1
          Length = 247

 Score =  139 bits (349), Expect = 7e-38
 Identities = 81/246 (32%), Positives = 132/246 (53%), Gaps = 8/246 (3%)

Query: 10  LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEASVTFYH 69
           + G+T+ I+GGA G+G       + +GA+V   DIL EE   L    K+  P+A++ F  
Sbjct: 7   VSGRTVLITGGARGMGEAHARLLVAEGARVVVGDILEEEGRALA---KELGPDAAL-FQP 62

Query: 70  CDLVDIAALKRVIAQVEDDLGPISVLINNAACDQRHSIDEVTPEYWDQCLNTNLRHYFFA 129
            D+   AA ++ ++  E+  GP+S L+NNA       I E++   + + ++ N    F  
Sbjct: 63  LDVTSEAAWQQAVSAAEEAFGPVSGLVNNAGIVHVGPIAELSEADYRKVVDVNQVGVFLG 122

Query: 130 VQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGKDKIRIN 189
           +++V P M+R GGGS++N+ S+      +G+ GYTA+K    G+T+  A + G+  IR+N
Sbjct: 123 MKSVLPSMRRAGGGSIVNISSVGGIIAFSGIVGYTAAKWAVRGMTKTAAQEFGRYGIRVN 182

Query: 190 TLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKLCTAQNF 249
           ++ PG V T         +    H+     I     PE++A M LFL +D+S  CT   F
Sbjct: 183 SVHPGMVATPMTADAPGTEGAVAHLP----IPRQARPEELATMVLFLLSDESSYCTGGEF 238

Query: 250 IVDGGW 255
            VDGG+
Sbjct: 239 TVDGGY 244


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: 150
Number of extensions: 7
Number of successful extensions: 3
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: 247
Length adjustment: 24
Effective length of query: 232
Effective length of database: 223
Effective search space:    51736
Effective search space used:    51736
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: 46 (22.3 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