GapMind for Amino acid biosynthesis

 

Alignments for a candidate for fbp in Desulfovibrio vulgaris Hildenborough

Align Fructose-bisphosphate aldolase class 1; EC 4.1.2.13; Fructose-bisphosphate aldolase class I; FBP aldolase (uncharacterized)
to candidate 209396 DVU0460 predicted phospho-2-dehydro-3-deoxyheptonate aldolase

Query= curated2:Q9V2I6
         (281 letters)



>MicrobesOnline__882:209396
          Length = 266

 Score =  174 bits (440), Expect = 2e-48
 Identities = 102/275 (37%), Positives = 157/275 (57%), Gaps = 13/275 (4%)

Query: 6   NIGIKRRLRRFFRRD-GRALIFAMDHGFEHGPTDFEPVWEHVNPRVIIRKVVRAGVDGVM 64
           +IG K R+ R F R  GR++I  +DHG   GP D       V+ R  + +V   G D V+
Sbjct: 2   HIGKKIRMERLFNRTTGRSVIVPLDHGVSVGPID-----GLVDMRDTVNQVAEGGADAVL 56

Query: 65  MLPGMARIAGDDVKPEVGLMIKITSKTNLRPKAEQLMQSQLAFVEDAIKLGADAIAATVY 124
           M  G+ R    +   +VGL++ +++ T+L P      ++  A VEDAIK GAD ++  V 
Sbjct: 57  MHKGLVRCGHREGGRDVGLIVHLSASTSLSPLPNA--KTLTATVEDAIKHGADGVSVHVN 114

Query: 125 WGSPQEDAMMRQFAEIVSYAHDLGFPVVQFAYPRGPYIDEKYGRKEDYRVVMYGARAAAE 184
            G   E  M+     + + A+D G P++   Y RGP I ++Y    D +VV + AR   E
Sbjct: 115 LGDETERDMLADLGRVATIANDWGVPLLAMMYARGPRIRDQY----DPQVVAHCARVGVE 170

Query: 185 MGADMIKTYWTGSRETFAKVVDAAAGVPVLLSGGAKAENPLDFLKVVYEVIEAGGSGAVV 244
           +GAD++K  +TG  +TFA VV +   VPV+++GG K ++  DFL++V++ + AGGSG  V
Sbjct: 171 LGADVVKVPYTGDMDTFAHVVQSCC-VPVVIAGGPKLDSTRDFLQMVHDAVRAGGSGLSV 229

Query: 245 GRNIFQRENPEPMIKALIRVIHRNEDPEEAAKAEG 279
           GRNIFQ   P  ++KA+  ++H + D E+A    G
Sbjct: 230 GRNIFQHARPSQLVKAVRGLVHEDWDVEQAIAIVG 264


Lambda     K      H
   0.321    0.138    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: 231
Number of extensions: 18
Number of successful extensions: 5
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: 281
Length of database: 266
Length adjustment: 25
Effective length of query: 256
Effective length of database: 241
Effective search space:    61696
Effective search space used:    61696
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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