GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas fluorescens FW300-N2C3

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate AO356_28585 AO356_28585 ABC transporter

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28585
          Length = 379

 Score =  315 bits (806), Expect = 2e-90
 Identities = 179/379 (47%), Positives = 237/379 (62%), Gaps = 22/379 (5%)

Query: 1   MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60
           +++L L+++ K+   +    + D  L+I   EF+VFVGPSGCGKST LR++AGL+ I  G
Sbjct: 1   VIKLKLDNVNKQLGGAR--ILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGG 58

Query: 61  ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120
           +L IDG  VND  P++R + MVFQ+YALYPHMSVYDN++FGLKL    K ++ +RV + A
Sbjct: 59  DLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTA 118

Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
           QIL L + L+RKP +LSGGQRQRVAMGRA+ R+  + L DEPLSNLDA LRV MR EIA+
Sbjct: 119 QILQLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240
           +H R+G+T IYVTHDQ EAMTLAD+IV+++           GR+EQVG+P+ELY RPA++
Sbjct: 179 LHGRLGSTMIYVTHDQVEAMTLADKIVVLNG----------GRIEQVGSPRELYERPASR 228

Query: 241 FVAGFIGSPAMNFFDVTI-KDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPED 299
           FVAGF+GSP MNF    +   G     + L + +T   L    S    N  L  GIRPE 
Sbjct: 229 FVAGFLGSPRMNFLAAFLHTPGETSQVESLVLGMT--SLPFDSSGLAANTQLSLGIRPEH 286

Query: 300 ISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTE-FAARVDARDFHEPGEKVSL 358
           I+            T    V   E LGSET ++L  GQ +    R +       G++V L
Sbjct: 287 IALKA------AQGTAGIAVSGVEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVEL 340

Query: 359 TFNVAKGHFFDAETEAAIR 377
             ++   H FD    A  R
Sbjct: 341 QLDIDNLHVFDTHGTALQR 359


Lambda     K      H
   0.318    0.135    0.375 

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: 342
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: 379
Length adjustment: 30
Effective length of query: 347
Effective length of database: 349
Effective search space:   121103
Effective search space used:   121103
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: 50 (23.9 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