GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylC in Dinoroseobacter shibae DFL-12

Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate 3607832 Dshi_1240 SMP-30/Gluconolaconase/LRE domain protein (RefSeq)

Query= metacyc::MONOMER-20630
         (291 letters)



>FitnessBrowser__Dino:3607832
          Length = 286

 Score =  126 bits (316), Expect = 6e-34
 Identities = 97/290 (33%), Positives = 138/290 (47%), Gaps = 12/290 (4%)

Query: 1   MTVTRVVDTSCRLGEGPVWHPDEKRLYWVDIESGRLHRYDPETGAHDCPVETSVIAGVTI 60
           M+ T   D  C LGEGP+WHP+ ++L+W DI   R+   D +T   +   +  V A   +
Sbjct: 1   MSATLYDDRPCALGEGPLWHPERQQLFWFDITGQRMLSRDGDTPL-EWQFDEMVSAAGWV 59

Query: 61  QRDGSLLAFMDRGRVGRVVDGDRRESARI-VDSP-TRFNDVIADPAGRVFCGTM--PSDT 116
             D  L+A         + +G+ R  A +  D P TR ND  ADP G  + GTM   ++ 
Sbjct: 60  DHDTLLIASETALVTFDLAEGESRFVAPLEADRPETRSNDGRADPWGGFWIGTMGKSAEP 119

Query: 117 AGGRLFRLDTDGTVTTVETGVGIPNGMGFTRDRERFYFTETEARTVYRYAYDEETGAVSA 176
             G ++RL  DGT+  V   V I N + F   +   Y+ +T  R V R   D + G  S 
Sbjct: 120 GAGAIYRL-FDGTLRRVVRDVTISNALCFDAAQSCAYYADTPTRQVMRLPLDGD-GWPSG 177

Query: 177 RERFVESPETPGL-PDGMTVDSAGHIWSARWEGGCVVEYDADGTELGRFDVPTEKVTSVA 235
                      GL PDG   D+AG++W A+W  G V  +  DGT L          +  A
Sbjct: 178 PATVAVDLRAEGLNPDGAVTDAAGNLWIAQWGAGRVACHAPDGTFLRALACGGRHSSCPA 237

Query: 236 FGGPDLDSLYVTTAGGDGDGSAGEGDESTGDAAGALFRLDVAATGRPEFR 285
           FGGPDLD L++TTA    +G + + D +     G +F  +  A G PE R
Sbjct: 238 FGGPDLDQLFITTA---REGLSAD-DIAAAPENGCVFAAEGVARGLPEPR 283


Lambda     K      H
   0.317    0.138    0.420 

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: 266
Number of extensions: 21
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: 291
Length of database: 286
Length adjustment: 26
Effective length of query: 265
Effective length of database: 260
Effective search space:    68900
Effective search space used:    68900
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 (21.6 bits)
S2: 48 (23.1 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