GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Pseudomonas fluorescens FW300-N2E3

Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate AO353_04045 AO353_04045 3-ketoacyl-ACP reductase

Query= reanno::Koxy:BWI76_RS01745
         (267 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04045
          Length = 252

 Score =  124 bits (310), Expect = 3e-33
 Identities = 84/267 (31%), Positives = 144/267 (53%), Gaps = 26/267 (9%)

Query: 5   LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSG-------NYNFWP 57
           + L +K+I +TGG  G+G ++ +   A+GA + ++D++     Q+             + 
Sbjct: 1   MKLTDKVIIITGGCQGLGRSMAEYFAAKGAKLALVDLNQEKLDQAVAACKAAGVEARAYL 60

Query: 58  TDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVN 117
            ++++  +V   V  + + FG I GL+NNAG+    LL+  K      +++ A ++ +++
Sbjct: 61  CNVANEEQVTHMVAQVAEDFGAIHGLINNAGILRDGLLIKVK-DGEMTKMSLAQWQAVID 119

Query: 118 INQKGVFLMSQAVARQMVKQRSG-VIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSK 176
           +N  GVFL ++ VA +M++ ++G  IVN+SS S   G+ GQ+ Y+A KA + + T +W+K
Sbjct: 120 VNLTGVFLCTREVAAKMIELKTGGAIVNISSISRA-GNVGQTNYSAAKAGVAAATVTWAK 178

Query: 177 ELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLT 236
           EL +HGIRV G+APG +E T +      EAL        E++  G     IPL R G+  
Sbjct: 179 ELARHGIRVAGIAPGFIE-TEMTLSMKPEAL--------EKMTSG-----IPLKRMGKPE 224

Query: 237 EVADFVCYLLSERASYMTGVTTNIAGG 263
           E+A    Y+      Y TG    + GG
Sbjct: 225 EIAHSAAYIFEN--DYYTGRILEMDGG 249


Lambda     K      H
   0.315    0.132    0.378 

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: 183
Number of extensions: 5
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: 267
Length of database: 252
Length adjustment: 24
Effective length of query: 243
Effective length of database: 228
Effective search space:    55404
Effective search space used:    55404
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: 42 (22.0 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