GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115
          Length = 381

 Score =  311 bits (796), Expect = 2e-89
 Identities = 174/373 (46%), Positives = 241/373 (64%), Gaps = 28/373 (7%)

Query: 4   LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63
           LKLDN+ K+    +   + + +L+I   EF+VFVGPSGCGKST LR+IAGL+ I  G+L 
Sbjct: 4   LKLDNVNKQLGGMR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61

Query: 64  IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123
           ID + +ND  P++R + MVFQ+YALYPHMSVY+N++FGLKL K  K  + +RV + A+IL
Sbjct: 62  IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQIL 121

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183
            L + L+RKP +LSGGQRQRVAMGRA+ R+  + L DEPLSNLDA LRV MR EIA++H 
Sbjct: 122 QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHD 181

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243
           R+G+T IYVTHDQ EAMTLAD+IV+++           GR+EQ+G+P+ELY  PA++FVA
Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNG----------GRVEQVGSPRELYERPASRFVA 231

Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYL--GKKVTLGIRPEDIS 301
           GF+GSP MNF    ++      +  L   L  G   +  +   L  G  ++LGIRPE   
Sbjct: 232 GFLGSPRMNFLSARLQTP---GETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPE--- 285

Query: 302 SDQIVHETFPNASVTADILVS--ELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKVQL 358
                H +   A  TA ++V+  E LGSE+ ++++ G  E    R         G++V+L
Sbjct: 286 -----HVSLKAADGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVEL 340

Query: 359 TFNIAKGHFFDLE 371
             ++   H FD +
Sbjct: 341 LLDLDNLHLFDAD 353


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: 360
Number of extensions: 16
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: 381
Length adjustment: 30
Effective length of query: 347
Effective length of database: 351
Effective search space:   121797
Effective search space used:   121797
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.

Links

Downloads

Related tools

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