GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Sulfurimonas denitrificans DSM 1251

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011372993.1 SUDEN_RS07140 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000012965.1:WP_011372993.1
          Length = 237

 Score =  127 bits (319), Expect = 2e-34
 Identities = 78/221 (35%), Positives = 127/221 (57%), Gaps = 7/221 (3%)

Query: 4   LKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEV----- 58
           +KN  K      V+ N +  + +GE + +I PSG+GK+T +  +  + E +SGE+     
Sbjct: 13  VKNFGKNDSLVKVIDNASFEINKGELVALIAPSGAGKTTLLMMIGCVLEPTSGEIWLGEE 72

Query: 59  VVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFK 118
           VV N     K+   I R+    +FQ   L P + V++N+TL P ++ K S+KEA++ A +
Sbjct: 73  VVYNNKWIAKDTRRIRREKIGFIFQAHYLIPFLNVIENITLLP-QVNKVSEKEAKQKAME 131

Query: 119 YLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVM 178
            L+ + + DKA+  P+ LSGGQ QRVAIAR+L      IL DEPT+ALD      V+ ++
Sbjct: 132 LLEYLEIADKAHAMPSQLSGGQNQRVAIARALANNPEIILADEPTAALDAHRSISVIKML 191

Query: 179 KEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENI 219
           K+I+ + N  ++ VTH+        D+I+ +++  IV E +
Sbjct: 192 KKIAIEQNVAIITVTHDERIL-PYFDKIMKIQNRGIVFEEL 231


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: 128
Number of extensions: 9
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: 237
Length adjustment: 23
Effective length of query: 219
Effective length of database: 214
Effective search space:    46866
Effective search space used:    46866
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