GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Synechococcus elongatus PCC 7942

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  241 bits (615), Expect = 2e-68
 Identities = 140/326 (42%), Positives = 197/326 (60%), Gaps = 27/326 (8%)

Query: 21  AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVNDVEPKDRDI 80
           AVK+ +L VE    V LLGPSG GK+T LR+IAGLE+   G+I++ G+   +   +DR I
Sbjct: 17  AVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATNESVRDRQI 76

Query: 81  AMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPRQLSGG 140
             VFQ+YAL+ H+TV +N+AFGL+LRK+ K+++  RV E  +++ +  L DR P QLSGG
Sbjct: 77  GFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQLTGLGDRYPSQLSGG 136

Query: 141 QRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEA 200
           QRQRVA+ RA+   P+V L DEP   LDAK+R  +RS L+KLH  +  T ++VTHDQ EA
Sbjct: 137 QRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEA 196

Query: 201 MTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGGLWIQA 260
           M +AD+IVVM  G+++QIG+P EIY++PA  FV  FIG  P+N      V        QA
Sbjct: 197 MEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG--PVN------VLPNSSHIFQA 248

Query: 261 SGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTITGVVDVVEPLGSE 320
            G     P+ F               +RP DI     A+ P PE T+   +D +  LG E
Sbjct: 249 GGLDTPHPEVF---------------LRPHDIE---IAIDPIPE-TVPARIDRIVHLGWE 289

Query: 321 TILHVKVGDDLIVASVNPRTQAKEEQ 346
               V++ D  ++ +  PR + ++ Q
Sbjct: 290 VQAEVRLEDGQVLVAHLPRDRYRDLQ 315


Lambda     K      H
   0.319    0.138    0.387 

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: 1
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: 369
Length of database: 338
Length adjustment: 29
Effective length of query: 340
Effective length of database: 309
Effective search space:   105060
Effective search space used:   105060
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: 49 (23.5 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