GapMind for catabolism of small carbon sources

 

Alignments 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_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  297 bits (761), Expect = 3e-85
 Identities = 164/355 (46%), Positives = 221/355 (62%), Gaps = 25/355 (7%)

Query: 3   KIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62
           K++  N+ K  G   +L+ + L+IA GEF+V VGPSGCGKSTLLR +AGL+S   G + I
Sbjct: 3   KLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLI 62

Query: 63  DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISELLQ 122
           DG+++ND+EP+ R + MVFQSYALYPHM+V +N+ FGLKL       + +RV + +++LQ
Sbjct: 63  DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQ 122

Query: 123 IKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLHHN 182
           +  LL RKPKELSGGQRQRVA+GRA++R+  ++LFDEPLSNLDA LR QMR EI RLH  
Sbjct: 123 LDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDR 182

Query: 183 SKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMNFL 242
             STMIYVTHDQ+EA TL D+I VL  G +EQ+G+P E+Y RP + F+A F+GSP MNFL
Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMNFL 242

Query: 243 --------EGAVLEKIPW----------PEARKADQILGIRPDAFALNQGPLGTQEVALG 284
                   E ++++ + W            A      LGIRP+  +L     GT  V   
Sbjct: 243 SARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAAD-GTAGVV-- 299

Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRIL-VDSMDNFSMKQTLPLKIDLTKAHLFD 338
              +   E LG +  +H     +   I   +    +     + L +DL   HLFD
Sbjct: 300 ---VTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFD 351


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: 366
Number of extensions: 12
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: 381
Length adjustment: 29
Effective length of query: 318
Effective length of database: 352
Effective search space:   111936
Effective search space used:   111936
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