GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Azospirillum brasilense Sp245

Align Probable 2-methylisocitrate lyase 2; 2-MIC; MICL; (2R,3S)-2-methylisocitrate lyase; EC 4.1.3.30 (characterized)
to candidate AZOBR_RS27820 AZOBR_RS27820 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= SwissProt::Q8NSL2
         (307 letters)



>FitnessBrowser__azobra:AZOBR_RS27820
          Length = 290

 Score =  179 bits (453), Expect = 9e-50
 Identities = 103/255 (40%), Positives = 147/255 (57%), Gaps = 4/255 (1%)

Query: 12  TERRKALRAALAAPEIARMPGAFSPLAARAIQEAGFEGVYVSG-AVVAADLALPDIGLTT 70
           T   + L+ AL AP +  MP  F  L+AR I++AGF    +SG AV A  L +PD GL +
Sbjct: 2   TTPAQRLKTALEAPGLHLMPCCFDALSARLIEQAGFRVSLMSGFAVSATRLGMPDTGLIS 61

Query: 71  LTEVAHRSRQIARVTD-LPVLVDADTGFGEPMSAARTVSELEDAGVAGCHLEDQVNPKRC 129
             E+  + R + +    L V+ D DTG+G  M+  RTV +   AG A   +EDQV+PKRC
Sbjct: 62  FAEMLDQLRNVCQAAPGLLVIGDGDTGYGNAMNVQRTVRDYARAGAAAVLIEDQVSPKRC 121

Query: 130 GHLDGKEVVGTDIMVRRIAAAVNERRD--EQFVICARTDAAGVEGIDSAIERAKAYADAG 187
           GH  GK+VVG      +I AAV+  R      +I ARTDA  V G D+A+ER + + + G
Sbjct: 122 GHTKGKQVVGRAEARMKIRAAVDAARSGANDILILARTDARAVHGFDAALERCQDFVEEG 181

Query: 188 ADMIFTEALYSPADFEKFRAAVDIPLLANMTEFGKTELLPAQLLEDIGYNAVIYPVTLLR 247
           AD+IF EA +   +   F A +D P +ANM   G+T +LP + LE +G+    YP+TL+ 
Sbjct: 182 ADIIFMEAPHDETEMAAFCAGIDRPAMANMVRGGQTPMLPPRELEALGFKLAAYPLTLMS 241

Query: 248 IAMGQVEQALGDIAN 262
            A+  +  AL  +A+
Sbjct: 242 AAIDAMRAALAAVAD 256


Lambda     K      H
   0.320    0.134    0.382 

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: 223
Number of extensions: 16
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: 307
Length of database: 290
Length adjustment: 27
Effective length of query: 280
Effective length of database: 263
Effective search space:    73640
Effective search space used:    73640
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: 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