GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potD in Rhodobacter viridis JA737

Align Spermidine/putrescine ABC transporter, spermidine/putrescine-binding protein, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate WP_110806537.1 C8J30_RS14400 spermidine/putrescine ABC transporter substrate-binding protein

Query= TCDB::Q97Q45
         (356 letters)



>NCBI__GCF_003217355.1:WP_110806537.1
          Length = 340

 Score =  192 bits (489), Expect = 8e-54
 Identities = 107/305 (35%), Positives = 163/305 (53%), Gaps = 5/305 (1%)

Query: 31  SRDSQKLVIYNWGDYIDPELLTQFTEETGIQVQYETFDSNEAMYTKIKQGGTTYDIAIPS 90
           +R  + L +YNWGDYI+P +LT+FTEETGI+V  +T+ +NE M  KI+ G T YDI  PS
Sbjct: 18  ARAEETLALYNWGDYINPAVLTKFTEETGIKVTLDTYSANEEMLAKIQAGATGYDIVFPS 77

Query: 91  EYMINKMKDEDLLVPLDYSKIEGIENIGPEFLNQSFDPGNKFSIPYFWGTLGIVYNETMV 150
            +M + M   DLL   + +      NI P FL    DP + + +PY WGT+GI YNE + 
Sbjct: 78  VWMQDIMVKLDLLEQTNINADPAFANIDPAFLRSKEDPQSSYCLPYAWGTVGIFYNENVT 137

Query: 151 DEAPEHWDDLWKPEYK--NSIMLFDGAREVLGLGLNSLGYSLNSKDLQQLEETVDKLYKL 208
                 WDD +    K    I L D  REVLG+GL   G+S+NS D  +L+E  D +   
Sbjct: 138 GPI-AGWDDFFAIPQKTGQKITLLDDMREVLGMGLIMTGHSVNSTDPAELKEAADYVTAH 196

Query: 209 TPNIKAIVADEMKGYMIQNNVAIGVTFSGEASQMLEKNENLRYVVPTEASNLWFDNMVIP 268
              + A   + M   ++  +VA    F G  +     +  ++Y++P E + ++ +N+ + 
Sbjct: 197 KAEVTAFTYESMP-LLLSGDVAAAHYFVG-GNMFFVDHPEIKYIIPKEGATMYQENICVL 254

Query: 269 KTVKNQNSAYAFINFMLKPENALQNAEYVGYSTPNLPAKELLPEETKEDKAFYPDVETMK 328
           K   ++ +A  F+ F L+PE A  N       TPN PA +L P+  K +       ET+ 
Sbjct: 255 KDAPHKEAAQKFLQFYLRPEIAALNVSQQFNGTPNRPANDLTPDFIKSNPNINVPAETLA 314

Query: 329 HLEVY 333
            L+++
Sbjct: 315 RLQIF 319


Lambda     K      H
   0.316    0.135    0.397 

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: 358
Number of extensions: 23
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: 356
Length of database: 340
Length adjustment: 29
Effective length of query: 327
Effective length of database: 311
Effective search space:   101697
Effective search space used:   101697
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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