GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas fluorescens FW300-N2E3

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 AO353_03840 AO353_03840 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03840
          Length = 351

 Score =  234 bits (597), Expect = 3e-66
 Identities = 136/301 (45%), Positives = 191/301 (63%), Gaps = 21/301 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           MT L L+N+ KRY  A   +V++ NL + + + + F+GPSGCGK+T LRMIAGLE ++ G
Sbjct: 1   MTGLILENVEKRYGTA--CAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + +DD+ + +     R+  MVFQ+ AL+PHM+V EN+A+ LKLR   K D   RV E  
Sbjct: 59  EIRLDDEDIGNTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKVDQQARVVELL 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           E++ L E ++R  A LSGGQRQRVA+ RAI    K+ L+DEPLS LDAKLR +M+ EI +
Sbjct: 119 ELIQLQEMIDRPVAKLSGGQRQRVAIARAIASHPKILLLDEPLSALDAKLRESMQVEIRQ 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           + +R+  TTI VTHDQ EAMT+AD +V++             R++Q+GTP E+Y  PAN+
Sbjct: 179 LQQRLNITTIMVTHDQREAMTMADIVVVLGQ----------NRVQQVGTPIEIYRHPANE 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVN-QDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED 299
           FVA FIGS   N F  T   +  V    G +L +P     +      +G+KV + +RPED
Sbjct: 229 FVADFIGSG--NIFPATALGDGKVGLPGGDALQVPICSSIV------VGEKVKMLVRPED 280

Query: 300 I 300
           +
Sbjct: 281 L 281


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: 320
Number of extensions: 10
Number of successful extensions: 4
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: 351
Length adjustment: 29
Effective length of query: 348
Effective length of database: 322
Effective search space:   112056
Effective search space used:   112056
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