GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_012411414.1 NPUN_RS25940 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000020025.1:WP_012411414.1
          Length = 254

 Score =  151 bits (382), Expect = 1e-41
 Identities = 93/230 (40%), Positives = 137/230 (59%), Gaps = 11/230 (4%)

Query: 1   MIELKNVNKYYGTHHV----LKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           +I L+N+ K YG+       L ++NL V++GE   I+GPSGSGKST +  +  L+  ++G
Sbjct: 21  IIRLENIFKIYGSGETEVRALNDVNLIVEQGEYCAIMGPSGSGKSTAMNIIGCLDRPTTG 80

Query: 57  EVVVNNL---VLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
              ++NL    ++ ++   I  K    VFQ F+L P +T L+N+ L PM     + KE  
Sbjct: 81  HYYLDNLDVAQMDDRSLAHIRNKKLGFVFQQFHLLPQLTALENVIL-PMLYAGVNPKERS 139

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
           + A   L  VGL ++ N  P  LSGGQQQRVAIAR++  +   +L DEPT ALD  T QE
Sbjct: 140 DRAIVALTRVGLANRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTGALDSRTTQE 199

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENI-PSE 222
           VLD+  E+ + S  T+V+VTHE   A++   RI++  DG +V  N+ PS+
Sbjct: 200 VLDIFSEL-NASGITVVMVTHEPEVARQ-TQRIVWFRDGQVVHSNLTPSD 247


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: 145
Number of extensions: 11
Number of successful extensions: 4
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