GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  140 bits (354), Expect = 4e-38
 Identities = 87/235 (37%), Positives = 137/235 (58%), Gaps = 7/235 (2%)

Query: 3   LALDSISKKVGAQTW-LYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61
           L +  +SK+  A +  L D SL ++ G V  ++G + +GK+SL+RI+AGL+  +AG V +
Sbjct: 4   LKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGVVHL 63

Query: 62  DGKDVTG-----MPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIAS 116
             + +       +P  D  + +++Q++  YP+  V  NIA PL L  +     R  EI  
Sbjct: 64  GDQKILNPAQKLVPGYDE-IQLIHQEYKLYPNSTVEENIARPLLLYDKAYQKERTAEILE 122

Query: 117 RLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQL 176
            L +  F D+ P +LSGGQQQ+VA+ RAL+    ++LLDEP  +LD   + +L EEL ++
Sbjct: 123 LLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIEELKEI 182

Query: 177 FAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAF 231
           F A + TV++ T +  +ALL+     ++ +G+LLQ G   EVF  P S  VAR F
Sbjct: 183 FDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237


Lambda     K      H
   0.318    0.133    0.375 

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: 218
Number of extensions: 10
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: 363
Length of database: 318
Length adjustment: 28
Effective length of query: 335
Effective length of database: 290
Effective search space:    97150
Effective search space used:    97150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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