GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Pseudomonas fluorescens FW300-N1B4

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate Pf1N1B4_914 ABC-type polar amino acid transport system, ATPase component

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_914
          Length = 254

 Score =  278 bits (712), Expect = 6e-80
 Identities = 139/241 (57%), Positives = 186/241 (77%), Gaps = 2/241 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           +I+++ VNK+YG  HVLK+INL+VK+GE++V+ GPSGSGKSTTIRC+N LEE   G +VV
Sbjct: 14  IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73

Query: 61  NNLVL-NHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           + + L N   +IE  R+   MVFQHFNL+PH+T+LQN TLAPM ++K  K++AEE A  Y
Sbjct: 74  DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           L+ V + ++A+ YP  LSGGQQQRVAIAR+LC K   +LFDEPTSALDPE ++EVLD M 
Sbjct: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
            ++ +   TM+ VTHEMGFA+ VA+R+IFM+ G IVE+  P++FF NP+ ER +LFL +I
Sbjct: 194 GLA-EDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNERTKLFLSQI 252

Query: 240 L 240
           L
Sbjct: 253 L 253


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: 192
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: 254
Length adjustment: 24
Effective length of query: 218
Effective length of database: 230
Effective search space:    50140
Effective search space used:    50140
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