GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Escherichia coli BW25113

Align Solute-binding protein Bpro_3107 (characterized)
to candidate 17640 b3579 predicted transporter (NCBI)

Query= SwissProt::Q128M1
         (330 letters)



>FitnessBrowser__Keio:17640
          Length = 328

 Score =  171 bits (434), Expect = 2e-47
 Identities = 109/327 (33%), Positives = 178/327 (54%), Gaps = 8/327 (2%)

Query: 11  IRSAALAALLAGLGM---GAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKI 67
           +RS   A  +AGL      +  A   R     +  D   +AA K+  +LL++++ G+ K+
Sbjct: 3   LRSVTYALFIAGLAAFSTSSLAAQSLRFGYETSQTDSQHIAAKKF-NDLLQERTKGELKL 61

Query: 68  KVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLD 127
           K+F    LG+ +  I  V+ G +D           + P+  +  +PFLF   AH  K+LD
Sbjct: 62  KLFPDSTLGNAQAMISGVRGGTIDMEMSGSNNFAGLSPVMNLLDVPFLFRDTAHAHKTLD 121

Query: 128 GPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVS 186
           G VGD++  S E  G   LA++++G R +  ++ P++T AD KGLKIR   S + +A   
Sbjct: 122 GKVGDDLKASLEGKGLKVLAYWENGWRDVTNSRAPVKTPADLKGLKIRTNNSPMNIAAFK 181

Query: 187 AMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMS 246
             GAN  PMP+ EVYTGL+T  IDA E+ I    +AK  E  K  S T H+ +P ++V++
Sbjct: 182 VFGANPIPMPFAEVYTGLETRTIDAQEHPINVVWSAKFFEVQKFLSLTHHAYSPLLVVIN 241

Query: 247 KIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIV-EVDKKSFQAV 305
           K  +D L    Q  + ++A+E+  ++R+   E + K +  +K AG E++ ++D+K+F   
Sbjct: 242 KAKFDGLSPEFQQALVSSAQEAGNYQRKLVAEDQQKIIDGMKEAGVEVITDLDRKAFSDA 301

Query: 306 MG-PVYDKFM-TTPDMKRLVKAVQDTK 330
           +G  V D F+   P    L+KAV + +
Sbjct: 302 LGNQVRDMFVKDVPQGADLLKAVDEVQ 328


Lambda     K      H
   0.316    0.130    0.362 

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: 221
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: 330
Length of database: 328
Length adjustment: 28
Effective length of query: 302
Effective length of database: 300
Effective search space:    90600
Effective search space used:    90600
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 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