GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Rhizobium johnstonii 3841

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000009265.1:WP_011654832.1
          Length = 254

 Score =  264 bits (674), Expect = 1e-75
 Identities = 136/242 (56%), Positives = 179/242 (73%), Gaps = 2/242 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MI ++ V K+YG    L++IN+SV+ GE++V+ GPSGSGKST IRC+N LE    GE+ V
Sbjct: 13  MITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCINHLETYERGEIRV 72

Query: 61  NNLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
             ++L ++ K I+  R+   MVFQ FNL+PH+TVLQN  LAPMK    S+ EAEE A   
Sbjct: 73  GGILLGNQAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKAVGVSRAEAEERARGL 132

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           L+ V +L++A+ YP  LSGGQQQRVAIAR+LC +   +LFDEPTSALDPE ++EVLD M 
Sbjct: 133 LERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTSALDPEMVKEVLDTMI 192

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
            ++ +   TM+ VTHEMGFA++VADR+IFM  GAIVEE  P+EFF+NP+ ER R FLG+I
Sbjct: 193 ALADE-GMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFTNPQHERTRKFLGEI 251

Query: 240 LK 241
           L+
Sbjct: 252 LR 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: 165
Number of extensions: 3
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 Apr 09 2024. 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