GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Pseudomonas stutzeri RCH2

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF3101 Psest_3160 ABC-type polar amino acid transport system, ATPase component

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__psRCH2:GFF3101
          Length = 255

 Score =  274 bits (700), Expect = 1e-78
 Identities = 138/241 (57%), Positives = 183/241 (75%), Gaps = 2/241 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           +I+++ V+K++G  HVLK+INLSV++GE++V+ GPSGSGKSTTIRC+N LEE   G +V+
Sbjct: 15  VIQMQGVHKWFGQFHVLKDINLSVRQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVI 74

Query: 61  NNLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           N + L    K IE  R    MVFQHFNL+PH+TVLQN TLAPM ++K  +++AEE A  Y
Sbjct: 75  NGVELTSDLKQIEAIRSEVGMVFQHFNLFPHLTVLQNCTLAPMWVRKLPRRQAEEIAMHY 134

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           L+ V + ++AN +P  LSGGQQQRVAIAR+LC K   +LFDEPTSALDPE ++EVLD M 
Sbjct: 135 LERVRIPEQANKFPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMV 194

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
            ++ +S  TM+ VTHEMGFA+ VADR+IFM+ G IVE+  P  FF+NP  +R +LFL +I
Sbjct: 195 SLA-ESGMTMLCVTHEMGFARTVADRVIFMDKGEIVEQAEPEMFFTNPVNDRTKLFLSQI 253

Query: 240 L 240
           L
Sbjct: 254 L 254


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: 181
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: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
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