GapMind for catabolism of small carbon sources

 

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

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_012411414.1 NPUN_RS25940 ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_000020025.1:WP_012411414.1
          Length = 254

 Score =  144 bits (364), Expect = 1e-39
 Identities = 88/224 (39%), Positives = 130/224 (58%), Gaps = 8/224 (3%)

Query: 1   MITLKNVSKWYG----HFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQG 56
           +I L+N+ K YG      + L D +  V++GE   + GPSGSGKST +  +  L+    G
Sbjct: 21  IIRLENIFKIYGSGETEVRALNDVNLIVEQGEYCAIMGPSGSGKSTAMNIIGCLDRPTTG 80

Query: 57  EITVDGI-VVNDKKTDLAKLRSR-VGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAR 114
              +D + V       LA +R++ +G VFQ F L P L+ +EN+ L  +      K  + 
Sbjct: 81  HYYLDNLDVAQMDDRSLAHIRNKKLGFVFQQFHLLPQLTALENVILPMLYAGVNPKERS- 139

Query: 115 EKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINE 174
           ++A+  L RVGL+   N  P QLSGGQQQRVAIARA+   P+ +L DEPT ALD     E
Sbjct: 140 DRAIVALTRVGLANRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTGALDSRTTQE 199

Query: 175 VLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDS 218
           VLD+  EL   G+T+++VTHE   AR+   R+++  +G++V  +
Sbjct: 200 VLDIFSELNASGITVVMVTHEPEVARQ-TQRIVWFRDGQVVHSN 242


Lambda     K      H
   0.320    0.135    0.383 

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: 146
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: 241
Length of database: 254
Length adjustment: 24
Effective length of query: 217
Effective length of database: 230
Effective search space:    49910
Effective search space used:    49910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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