GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c12640 in Shewanella oneidensis MR-1

Align D-lactate transporter, ATP-binding component (characterized)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::Phaeo:GFF1248
         (251 letters)



>lcl|FitnessBrowser__MR1:203044 SO3960 ABC transporter, ATP-binding
           protein (NCBI ptt file)
          Length = 243

 Score =  120 bits (301), Expect = 3e-32
 Identities = 75/246 (30%), Positives = 129/246 (52%), Gaps = 12/246 (4%)

Query: 4   LEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMFD 63
           L+ +N+ K +   Q + DV+L+V+   V  ++GPNGAGK+T    +VG +  D G +  D
Sbjct: 6   LKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHIFID 65

Query: 64  GKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSGQR 123
              +     +   + GI  + Q   IF  L+V +N+M     ++    E+N     S QR
Sbjct: 66  DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRK----ELN-----SDQR 116

Query: 124 DILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMARAD 183
           +  E  E +LEE ++   R     S+S G++RR+EI   L+  P+ +LLDEP AG+    
Sbjct: 117 E--EALEQLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLDEPFAGVDPIS 174

Query: 184 TNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPKVR 243
             +   +++Q+KS R + + I +H++     + +   +++ G+ + E  P  I  N +VR
Sbjct: 175 VIDIKKIIEQLKS-RGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTPAEILDNQQVR 233

Query: 244 EAYLGE 249
             YLGE
Sbjct: 234 AVYLGE 239


Lambda     K      H
   0.318    0.135    0.379 

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: 143
Number of extensions: 9
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: 251
Length of database: 243
Length adjustment: 24
Effective length of query: 227
Effective length of database: 219
Effective search space:    49713
Effective search space used:    49713
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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