GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Desulfovibrio vulgaris Miyazaki F

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Miya:8502394
          Length = 247

 Score =  124 bits (311), Expect = 2e-33
 Identities = 78/242 (32%), Positives = 124/242 (51%), Gaps = 7/242 (2%)

Query: 25  LLTGAAQGIGEAIVAAFASQQARLVISDI-QAEKVETVAAHWRERGADVHALKADVSNQQ 83
           L+TG ++GIG+A+    A +  ++ ++ + + E+ E VAA     G    A + DVS+  
Sbjct: 9   LVTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSDAA 68

Query: 84  DLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGCKAVLPQ 143
            + A  +  +     +DVLVN AG+      L M ++D+ R   ++L GA+   +     
Sbjct: 69  AVAAFFQEEIREKVTLDVLVNNAGITKDGLILRMKDDDFDRVLDVNLSGAFTCLREAAKL 128

Query: 144 MIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNAIAPGYI 203
           M  Q  G I+NI S        G   Y  AK GL+G+T++   E A + V VNA+APG+I
Sbjct: 129 MTRQRKGRIVNITSVVGQMGNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTVNAVAPGFI 188

Query: 204 ETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCITID 263
           ET +     +     Y      ++  P RR+GQP ++A    FLASD+A +I    I ++
Sbjct: 189 ETDMTAKLTDEVRAAY------IEAIPLRRLGQPQDIADAVAFLASDKAGYITGQVIAVN 242

Query: 264 GG 265
           GG
Sbjct: 243 GG 244


Lambda     K      H
   0.321    0.137    0.419 

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: 141
Number of extensions: 6
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: 272
Length of database: 247
Length adjustment: 24
Effective length of query: 248
Effective length of database: 223
Effective search space:    55304
Effective search space used:    55304
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 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