GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Cereibacter sphaeroides ATCC 17029

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>NCBI__GCF_000015985.1:WP_011842387.1
          Length = 266

 Score =  220 bits (560), Expect = 2e-62
 Identities = 114/249 (45%), Positives = 166/249 (66%), Gaps = 8/249 (3%)

Query: 1   MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60
           ++ L+ + K +G F+VL   S +V +GEVV + G SGSGKST ++++N +E  Q G +  
Sbjct: 7   LLRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQAGTMDF 66

Query: 61  D--------GIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAP 112
                    G   +  K  L KLR+ +GMVFQ + L+PH+++++N+  A + + +  +A 
Sbjct: 67  GDFHFDFRKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTLRRTPRAQ 126

Query: 113 AREKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMI 172
           A E+A  LL R+GL    + +PA+LSGGQQQRVAIARAL M P  MLFDE TSALDPE++
Sbjct: 127 AVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTSALDPELV 186

Query: 173 NEVLDVMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRA 232
           +EVL +M  LA +GMTM++VTHE+ FAR V++RV+F D+G + E  P D    +P+S R 
Sbjct: 187 HEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLRNPESPRL 246

Query: 233 KDFLAKILH 241
           + FL +ILH
Sbjct: 247 RQFLHRILH 255


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: 160
Number of extensions: 5
Number of successful extensions: 2
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: 266
Length adjustment: 24
Effective length of query: 217
Effective length of database: 242
Effective search space:    52514
Effective search space used:    52514
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