GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N2E2

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate Pf6N2E2_3321 Ornithine cyclodeaminase (EC 4.3.1.12)

Query= BRENDA::P9WP55
         (310 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3321
          Length = 317

 Score =  163 bits (413), Expect = 4e-45
 Identities = 98/277 (35%), Positives = 155/277 (55%), Gaps = 7/277 (2%)

Query: 30  IVAKLEFFNPANSVKDRIGVAMLQAAEQAGLIKPDTIILEPTSGNTGIALAMVCAARGYR 89
           +  K+E  NPA S+K +  +++++ +E+ GL+ P   ++E +SGN G+AL+M+CA RGY 
Sbjct: 22  VYLKIEGLNPAGSIKLKTAISLIEESERLGLLSPGRKVIESSSGNLGVALSMICAQRGYP 81

Query: 90  CVLTMPETMSLERRMLLRAYGAELILTPGAD---GMSGA-IAKAEELAKTDQRYFVPQQF 145
                   ++     L++AYGAE+I+    D   G  GA I   +E+ + D RYF   Q+
Sbjct: 82  FTCITDPNVNQVSVNLMKAYGAEVIVCDTRDRNGGFLGARITLIQEMIRQDPRYFWTNQY 141

Query: 146 ENPANPAIHRVTTAEEVWRDTDGKVDIVVAGVGTGGTITGVAQVIKERKPSARFVAVEPA 205
            NPANP  H   TA E+ +       + V G GT GT+ G A+ ++E+ P  + +AV+  
Sbjct: 142 ANPANPLAHYNRTAPEILQQHPNCKWLFV-GAGTTGTLIGCARYLREKAPEVKLIAVDTV 200

Query: 206 ASPVLSGGQKGPHPIQGIGAGFVPPVLDQDLVDEIITVGNEDALNVARRLAREEGLLVGI 265
            S       K    I G+G    P +L++DLV+ I  V   + + + R +A++ GLL+G 
Sbjct: 201 GSINFQEVPK-KRLIPGLGTSRRPEILERDLVEHIEFVDEVETIRMCRSVAQDYGLLLGG 259

Query: 266 SSGAATVAALQVARRPENAGKLIVVVLPDFGERYLST 302
           S+G   VA  ++ R+   AG  +VV+ PD GERYL T
Sbjct: 260 STGTVLVAVKRL-RKQIPAGDEVVVISPDMGERYLET 295


Lambda     K      H
   0.318    0.136    0.383 

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: 213
Number of extensions: 8
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: 310
Length of database: 317
Length adjustment: 27
Effective length of query: 283
Effective length of database: 290
Effective search space:    82070
Effective search space used:    82070
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 (21.7 bits)
S2: 48 (23.1 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