GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Chlorobaculum tepidum TLS

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_010932579.1 AYT24_RS04145 phosphate ABC transporter ATP-binding protein PstB

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_000006985.1:WP_010932579.1
          Length = 286

 Score =  132 bits (332), Expect = 8e-36
 Identities = 84/260 (32%), Positives = 140/260 (53%), Gaps = 15/260 (5%)

Query: 5   PAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCIN 64
           P +K      +  V   + + +YG+F  ++ +N +++      I GPSG GKST +R IN
Sbjct: 27  PERKAIAGGGKPHVVARDFSIYYGEFEAVKKVNAEILSKYVTAIIGPSGCGKSTFLRAIN 86

Query: 65  RLEE-----HQKGKIVVDGTELTNDLKKIDEV--RREVGMVFQHFNLFPHLTILENCTLA 117
           R+ +     H  G ++ DG ++    K  DEV  R+++GMVFQ  N FP  +I +N    
Sbjct: 87  RMNDLIPNCHTTGALMFDGEDIYG--KFTDEVLLRKKIGMVFQKPNPFPK-SIFDNIAYG 143

Query: 118 PIWVRKMPKKQAEEVAMHFLKRV----KIPEQANKYPGQLSGGQQQRVAIARSLCMNPKI 173
           P       KK+  E+    L++     ++ ++ +K    LSGGQQQR+ +AR+L + P+I
Sbjct: 144 PKLHGIKDKKKLSEIVEKSLRKAALWDEVSDRLDKNALGLSGGQQQRLCVARALAVEPEI 203

Query: 174 MLFDEPTSALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQ 233
           +L DEPTSALDP+   ++ D +  L     T++ VTH M  A +V++  +F  +G +VE 
Sbjct: 204 LLLDEPTSALDPKATAKIEDLIQEL-RGSYTIMIVTHNMQQASRVSDYTMFFYEGVLVEH 262

Query: 234 NEPAAFFDNPQHERTKLFLS 253
                 F  P+   T+ +++
Sbjct: 263 APTTQLFTRPKDSMTEDYIT 282


Lambda     K      H
   0.321    0.135    0.394 

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: 183
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: 257
Length of database: 286
Length adjustment: 25
Effective length of query: 232
Effective length of database: 261
Effective search space:    60552
Effective search space used:    60552
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 (21.9 bits)
S2: 47 (22.7 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