GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Bb in Pseudomonas fluorescens FW300-N1B4

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Pf1N1B4_2538 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= uniprot:Q6MNM2
         (347 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2538 Putrescine transport
           ATP-binding protein PotA (TC 3.A.1.11.1)
          Length = 374

 Score =  233 bits (593), Expect = 8e-66
 Identities = 125/280 (44%), Positives = 174/280 (62%), Gaps = 15/280 (5%)

Query: 4   IQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62
           + F  ++KS+ G   ++K ++LDI  GEFL L+GPSG GK+T L  LAG E+  +G I +
Sbjct: 15  VSFRGVQKSYDGENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 74

Query: 63  DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQ 122
            G+ IN++ P  RDI MVFQ+YAL+PHMTVAEN+ F L ++ L   +++ RV  +  ++Q
Sbjct: 75  AGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRGLNKNDVSDRVKRVLSMVQ 134

Query: 123 IKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHN 182
           +     R P +LSGGQ+QRVAL RAL  +  ++L DEPL  LD  LR  M++EIK LH  
Sbjct: 135 LDTFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 194

Query: 183 SKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242
              T++YVTHDQ EA T+ DR+AV   G I+QI  P  +Y  PKNTF+A FIG  E N L
Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAPPRSLYEEPKNTFVANFIG--ENNRL 252

Query: 243 EGAVLEKIPWPEARKADQIL-----GIRPDAFALNQGPLG 277
            G +        +   D+ +     G + +A A+N G  G
Sbjct: 253 NGRL-------HSHTGDRCVVELGRGEKVEALAVNVGKTG 285


Lambda     K      H
   0.318    0.136    0.383 

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: 306
Number of extensions: 16
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: 347
Length of database: 374
Length adjustment: 29
Effective length of query: 318
Effective length of database: 345
Effective search space:   109710
Effective search space used:   109710
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 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