GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Shewanella loihica PV-4

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__PV4:5210736
          Length = 241

 Score =  255 bits (652), Expect = 5e-73
 Identities = 128/242 (52%), Positives = 180/242 (74%), Gaps = 2/242 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MI++ N++KY+G + VLK I+ S+  GE + +IGPSGSGKST +RC+N LE+ + GE+V+
Sbjct: 1   MIKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVI 60

Query: 61  NNLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           +   +   +  I+  R+   MVFQ+FNL+PH TV QN+TLAP+KL   ++ EA+  A + 
Sbjct: 61  DGQSITAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQAEADSEAMRL 120

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           L  VGL DKA+ YPA+LSGGQ+QRVAIAR+L  K   +LFDEPTSALDPE + +VLDVMK
Sbjct: 121 LDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGDVLDVMK 180

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
           +++ Q+  TMV+VTHEMGFAK+V+DR+IFM+ G +VE N+P+  F  P+  R + FL K+
Sbjct: 181 QLA-QAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQPQEPRTQAFLSKV 239

Query: 240 LK 241
           L+
Sbjct: 240 LR 241


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: 169
Number of extensions: 6
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: 241
Length adjustment: 23
Effective length of query: 219
Effective length of database: 218
Effective search space:    47742
Effective search space used:    47742
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