GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sphingomonas koreensis DSMZ 15582

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score =  125 bits (314), Expect = 8e-34
 Identities = 87/228 (38%), Positives = 125/228 (54%), Gaps = 11/228 (4%)

Query: 2   ITLKNVSKWYG----HFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGE 57
           I  + VSK Y       Q+L   S  V  GE+ +V GPSG GKSTL+  ++GL    QGE
Sbjct: 9   IDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGE 68

Query: 58  ITVDGIVVNDKKT---DLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAR 114
           +   G  +   K    D  +L +  G VFQ F LF  L+  E +    ++ +K   A AR
Sbjct: 69  VDALGNPICRMKAGARDAFRL-ANTGFVFQGFNLFNALTAEEQVAYV-LQCMKVKPAEAR 126

Query: 115 EKALKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINE 174
           ++A   LE VGL       P +LSGG++QRVAIARAL   P  +  DEPTSALD    + 
Sbjct: 127 QRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHA 186

Query: 175 VLDVMVELA-NEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKD 221
           V+ ++ ++A N+G  ++ VTH+       A+R+I M++G+I+ D   D
Sbjct: 187 VIALLRDIAHNQGAAVLCVTHDPRLL-SFADRIIHMEDGRIIRDERPD 233


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: 127
Number of extensions: 5
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: 243
Length adjustment: 23
Effective length of query: 218
Effective length of database: 220
Effective search space:    47960
Effective search space used:    47960
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 Sep 17 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