GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Pseudomonas simiae WCS417

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF1168 PS417_05935 polyamine ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__WCS417:GFF1168
          Length = 344

 Score =  227 bits (579), Expect = 3e-64
 Identities = 123/250 (49%), Positives = 163/250 (65%), Gaps = 4/250 (1%)

Query: 25  NLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMVFQ 84
           ++DIQD EF   +GPSG GKTT LR+IAG E  + G++ I       +PP  RD+  VFQ
Sbjct: 24  SIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIRIHGEEAAGLPPYQRDVNTVFQ 83

Query: 85  NYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQRV 144
           +YAL+PHM V  N+A+GLK++ V K E   R +EA  ++ +    DRKP  LSGGQRQRV
Sbjct: 84  DYALFPHMNVRDNVAYGLKVKGVGKTERMNRAEEALGMVALGGYGDRKPVQLSGGQRQRV 143

Query: 145 ALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTMGD 204
           AL RA+V  P+V L+DEPL  LD KLR QM++E++KL ++L  T I+VTHDQTEA++M D
Sbjct: 144 ALARALVNRPRVLLLDEPLGALDLKLREQMQSELKKLQRQLGITFIFVTHDQTEALSMSD 203

Query: 205 RIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ--DGDAFYFRAPSI 262
           R+ V   G I+Q DTP+ +Y +P   FVA F+G+   N IRGE+ Q   G A  F     
Sbjct: 204 RVAVFNKGRIEQVDTPRNLYMKPATSFVAEFVGT--SNVIRGELAQRLGGTAQPFSIRPE 261

Query: 263 SLRLPEGRYG 272
            +R  EG  G
Sbjct: 262 HVRFAEGPLG 271


Lambda     K      H
   0.321    0.138    0.395 

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: 340
Number of extensions: 13
Number of successful extensions: 1
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: 384
Length of database: 344
Length adjustment: 29
Effective length of query: 355
Effective length of database: 315
Effective search space:   111825
Effective search space used:   111825
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 (21.8 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