GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Acidovorax sp. GW101-3H11

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Ac3H11_1958 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1958
          Length = 245

 Score =  214 bits (545), Expect = 1e-60
 Identities = 118/244 (48%), Positives = 166/244 (68%), Gaps = 5/244 (2%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MIELKNV+K+YG   VL   + ++ +GE +V+ GPSGSGKST I+ +N LE    GE+ V
Sbjct: 1   MIELKNVSKWYGPVQVLNECSATINKGEVVVVCGPSGSGKSTLIKTINALEPFQKGEITV 60

Query: 61  NNLVLNHKN-KIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           + + L+  +  +   R    MVFQHF L+PH++V  NLT+A +K+  +S  EA++   K 
Sbjct: 61  DGVKLHDPSTNLPKLRSRVGMVFQHFELFPHLSVTDNLTIAQIKVLGRSADEAKKRGLKM 120

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           L+ VGL+   + +P  LSGGQQQRVAIAR+L      +LFDEPTSALDPE + EVLDVM 
Sbjct: 121 LERVGLIAHKDKFPGQLSGGQQQRVAIARALSMDPIVMLFDEPTSALDPEMVGEVLDVMV 180

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFME-DGAIVEENIPSEFFSNP--KTERARLFL 236
            ++++   TM+ VTHEMGFA++V++R+IFM+  G I+E+    EFF+NP  +  R + FL
Sbjct: 181 GLANE-GMTMMCVTHEMGFARKVSNRVIFMDVGGKILEDCSKDEFFNNPDARQPRTKDFL 239

Query: 237 GKIL 240
            KIL
Sbjct: 240 NKIL 243


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: 158
Number of extensions: 7
Number of successful extensions: 4
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: 245
Length adjustment: 24
Effective length of query: 218
Effective length of database: 221
Effective search space:    48178
Effective search space used:    48178
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