GapMind for catabolism of small carbon sources

 

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

Align Citrate lyase subunit beta; Citrase beta chain; Citrate (pro-3S)-lyase subunit beta; Citryl-CoA lyase subunit; EC 4.1.3.6; EC 4.1.3.34 (characterized)
to candidate Pf6N2E2_1831 Citrate lyase beta chain (EC 4.1.3.6)

Query= SwissProt::P0A9I1
         (302 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1831
          Length = 299

 Score =  144 bits (363), Expect = 2e-39
 Identities = 99/281 (35%), Positives = 149/281 (53%), Gaps = 5/281 (1%)

Query: 15  RSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDIETI 74
           RS+LFVP         +    ADA + DLEDSVA  +K  AR     A Q+   R ++ +
Sbjct: 9   RSLLFVPAHIGKFTEKAHERNADACILDLEDSVAPGQKTQARDAASSAAQNISNRGLDVL 68

Query: 75  VRVNALDSEWGVNDLEAVVRGGADVVRLPKTDTAQDVLDIEKEILRIEKACGREPGSTGL 134
           VR+N LDS  G+ DL+A+V      V LPK  +A+ V  +  ++ R+E   G + G T +
Sbjct: 69  VRINTLDSG-GLLDLQAIVSPAVCAVVLPKVASAEVVRHVALQLDRLETERGMDAGQTLI 127

Query: 135 LAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFARCSILQAAR 194
           LA IE    +    EIA AS RL+G++LG ED+  +   E  PE   LL+    +  A R
Sbjct: 128 LAQIEDVAALPLLDEIATASPRLMGMSLGPEDFSVSAGMEPVPE--TLLWPNQQVAFACR 185

Query: 195 SAGIQ--AFDTVYSDANNEAGFLQEAAHIKQLGFDGKSLINPRQIDLLHNLYAPTQKEVD 252
            AGI    F    +D ++   F Q     +QLG  G   I+P Q+ +L+ +++P   EV+
Sbjct: 186 RAGILPFGFPGSIADFSDIPRFRQALVLGRQLGMIGAFCIHPEQVAVLNEVFSPGDAEVE 245

Query: 253 HARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSR 293
           ++  ++     A  EG G  +  GKM+D P++ RAR +L+R
Sbjct: 246 YSVALLAEYACAEAEGRGAFAFRGKMIDAPIVARARELLTR 286


Lambda     K      H
   0.318    0.134    0.369 

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: 180
Number of extensions: 10
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: 302
Length of database: 299
Length adjustment: 27
Effective length of query: 275
Effective length of database: 272
Effective search space:    74800
Effective search space used:    74800
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 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