GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Pseudomonas fluorescens FW300-N2E2

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Pf6N2E2_3921 Cystine ABC transporter, ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3921
          Length = 253

 Score =  216 bits (551), Expect = 3e-61
 Identities = 115/247 (46%), Positives = 160/247 (64%), Gaps = 8/247 (3%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MI ++ + K +    VL  I+L ++EGE + IIGPSGSGK+T +RC+N LEE SSG + V
Sbjct: 1   MIVVEKLTKQFKGQVVLNGIDLKIEEGEVVAIIGPSGSGKTTFLRCLNFLEEPSSGRIKV 60

Query: 61  NNLVLN-------HKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
            ++ ++        +  +   R+    VFQ+FNL+PH T L+N+T  P  ++K  + EAE
Sbjct: 61  GDIEIDGSRPLNQQQGLVRRLRQQVGFVFQNFNLFPHRTALENVTEGPQVVKKIPRTEAE 120

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
               K L  VGL  K + YP  LSGGQQQRVAIAR+L  +   ILFDEPTSALDPE + E
Sbjct: 121 ALGRKLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPAVILFDEPTSALDPELVGE 180

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERAR 233
           VL  +++++ +   TMV+VTHEMGFA++VA+R++F + G IVE+      F+ PK ER R
Sbjct: 181 VLATIRDLAEEKR-TMVIVTHEMGFARDVANRVVFFDKGVIVEQGEAKALFAAPKEERTR 239

Query: 234 LFLGKIL 240
            FL K L
Sbjct: 240 QFLSKFL 246


Lambda     K      H
   0.317    0.133    0.372 

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: 167
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: 242
Length of database: 253
Length adjustment: 24
Effective length of query: 218
Effective length of database: 229
Effective search space:    49922
Effective search space used:    49922
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: 46 (22.3 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