GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK in Shewanella sp. ANA-3

Align ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= BRENDA::P68187
         (371 letters)



>lcl|FitnessBrowser__ANA3:7026050 Shewana3_3192 sulfate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 376

 Score =  215 bits (547), Expect = 2e-60
 Identities = 108/238 (45%), Positives = 157/238 (65%), Gaps = 4/238 (1%)

Query: 3   SVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFI 62
           S++L N++K +G+      +NLDI EGE +  +GPSG GK+TLLR+IAGLE   SG +  
Sbjct: 2   SIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHF 61

Query: 63  GEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAK----KEVINQRVNQVA 118
           G + +      +R VG VFQ+YAL+ H++VA+N++FGL++   K    K  I +RV+ + 
Sbjct: 62  GNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLL 121

Query: 119 EVLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISR 178
           E++QL HL  R P+ LSGGQ+QR+A+ R L  +P V LLDEP   LDA +R ++R  +  
Sbjct: 122 EMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRS 181

Query: 179 LHKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGS 236
           LH  L  T ++VTHDQ EA+ L+D++VV+  G + QV  P+ELY  P  RFV  F+G+
Sbjct: 182 LHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN 239


Lambda     K      H
   0.320    0.137    0.393 

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: 350
Number of extensions: 16
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: 371
Length of database: 376
Length adjustment: 30
Effective length of query: 341
Effective length of database: 346
Effective search space:   117986
Effective search space used:   117986
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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