GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Amantichitinum ursilacus IGB-41

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_001294205.1:WP_053938866.1
          Length = 242

 Score =  238 bits (606), Expect = 1e-67
 Identities = 123/241 (51%), Positives = 171/241 (70%), Gaps = 2/241 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           MI +KN++K+YG   VL + +  VK+GE +V+ GPSGSGKST I+C+NGLE    G+++V
Sbjct: 1   MISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIV 60

Query: 61  NNL-VLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           +   V + K  +   R    MVFQ+F L+PH+++ QNLTLA M++  +++ EA     + 
Sbjct: 61  DGTSVGDPKTNLPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRNRDEATVNGLRL 120

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

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
           E++ Q   TM+ VTHEMGFA++VA+R+IFM+ GAIVE+    +FF +P++ERA++FL KI
Sbjct: 181 ELA-QEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFGSPRSERAQVFLSKI 239

Query: 240 L 240
           L
Sbjct: 240 L 240


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: 149
Number of extensions: 4
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: 242
Length adjustment: 23
Effective length of query: 219
Effective length of database: 219
Effective search space:    47961
Effective search space used:    47961
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 24 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