GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas fluorescens GW456-L13

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830
          Length = 361

 Score =  232 bits (592), Expect = 1e-65
 Identities = 131/317 (41%), Positives = 196/317 (61%), Gaps = 27/317 (8%)

Query: 2   TTLKLDNIYKRYPNAKHYS--VENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITE 59
           T +++ N+ KRY +    +  ++N ++DI D EF   +GPSGCGK+T LR IAG E +++
Sbjct: 5   TAIEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSD 64

Query: 60  GNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEA 119
           G + +  + +ND  P  R +  VFQ+YAL+PHMSV +N+AFGL+++   +  I +RV E 
Sbjct: 65  GEIRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEM 124

Query: 120 AEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIA 179
             ++ +    +RKPA+LSGGQ+QRVA+ RA+    KV L+DEPLS LD KLR  M+ E+ 
Sbjct: 125 LALVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELK 184

Query: 180 KIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239
           ++ +  G T I+VTHDQ EA+TL+DRI +MSA          G+I QIG+P E+Y  P +
Sbjct: 185 RVQKEAGITFIFVTHDQEEALTLSDRIAVMSA----------GKILQIGSPNEIYERPQH 234

Query: 240 KFVAGFIGSPAMNFFEVTVEK----ERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGI 295
           +FVA FIG   +NF    +++    E+L   +G+ + +P         +G+ G KV L  
Sbjct: 235 QFVAQFIGD--INFLPGHIKRGQQNEKLFVPNGMPVEIP------CPAQGFDGSKVQLAF 286

Query: 296 RPEDISSDQIVHETFPN 312
           RPE     Q+V  T P+
Sbjct: 287 RPE---RSQLVEPTQPH 300


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: 324
Number of extensions: 7
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: 377
Length of database: 361
Length adjustment: 30
Effective length of query: 347
Effective length of database: 331
Effective search space:   114857
Effective search space used:   114857
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: 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