GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Pseudomonas simiae WCS417

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate GFF2270 PS417_11575 spermidine/putrescine ABC transporter ATPase

Query= TCDB::P96483
         (377 letters)



>FitnessBrowser__WCS417:GFF2270
          Length = 342

 Score =  240 bits (612), Expect = 5e-68
 Identities = 126/296 (42%), Positives = 187/296 (63%), Gaps = 24/296 (8%)

Query: 1   MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60
           MA +  +  ++ Y   D  AV   D+A+E GEF+ L+GPSGCGK+T+L+M+AG  DV+GG
Sbjct: 1   MAFLQLNALSKRYGAVD--AVVATDLAVEKGEFVSLLGPSGCGKTTTLQMIAGFVDVSGG 58

Query: 61  AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120
            I +  RD+TH  P  R + +VFQ+YAL+PHM+V DN+ F LK+  VP AEI  KV+   
Sbjct: 59  QILLDGRDITHAKPASRGLGVVFQSYALFPHMSVRDNVAFGLKMRKVPAAEIASKVKTVL 118

Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180
           +++ L  + DR P+ LSGGQRQRVA+ RA+V EP V L+DEPLSNLDA LR   + +I  
Sbjct: 119 ELVRLAPHADRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRR 178

Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240
           +Q  +GITT+ VTHDQ EA+++ DRV V++ G + Q+D+P  +Y+ P   F++ F+G   
Sbjct: 179 IQCAVGITTLMVTHDQAEALSISDRVVVMQAGRVTQIDAPYKLYEHPRTRFISDFVGKA- 237

Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAA----DKGDRTVTVGVRPEHFDVVELG 292
                            +++P + + L +     + GD  +T+ +RPE   +V+ G
Sbjct: 238 -----------------NLLPGDYDLLGSPQVRHESGDGELTLSLRPEKIQLVDAG 276


Lambda     K      H
   0.317    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: 328
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: 377
Length of database: 342
Length adjustment: 29
Effective length of query: 348
Effective length of database: 313
Effective search space:   108924
Effective search space used:   108924
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