GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>FitnessBrowser__Cola:Echvi_2204
          Length = 240

 Score =  131 bits (329), Expect = 1e-35
 Identities = 81/223 (36%), Positives = 122/223 (54%), Gaps = 8/223 (3%)

Query: 1   MISIKSINKWY----GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56
           +I  K I K Y       Q L   + ++ KGE +   GPSGSGKSTL+  +  L+    G
Sbjct: 4   IIETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAG 63

Query: 57  DIVVDGTSIADPKTN-LPKLRSR-VGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEAT 114
           + +++   ++    N L ++R++ +G VFQ F L P  T  EN+ +  I   G SK +  
Sbjct: 64  NYILNNKDVSHMTENELAEIRNKEIGFVFQTFNLLPRATCLENVALPLIYA-GYSKSDRE 122

Query: 115 KKGLQLLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNE 174
            K    L+ VGL    H  P +LSGGQ+QRVAIARAL  DP ++L DEPT  LD +   +
Sbjct: 123 DKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTSYD 182

Query: 175 VLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217
           ++++  +L  +G T++ VTHE   A   A R++ +  G +  D
Sbjct: 183 IMNLFDELHQKGNTIIMVTHEDDIAH-YAHRIVRLRDGLVETD 224


Lambda     K      H
   0.321    0.136    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: 131
Number of extensions: 7
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: 244
Length of database: 240
Length adjustment: 23
Effective length of query: 221
Effective length of database: 217
Effective search space:    47957
Effective search space used:    47957
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: 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