GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28585 AO356_28585 ABC
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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