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_1406 Synpcc7942_1406 ATPase

Query= TCDB::Q9X103
         (369 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  203 bits (517), Expect = 5e-57
 Identities = 127/340 (37%), Positives = 190/340 (55%), Gaps = 24/340 (7%)

Query: 8   LENVTKVYE-NKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYID 66
           L+ V K +  + + AV   +  +E  E + L+GPSGCGKTT LRMIAG E +  G I + 
Sbjct: 9   LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68

Query: 67  GKVV----NDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122
           G+ V      + P+ R + MVFQ+YAL+PH+TV +N+ FGL+ RK          R+A  
Sbjct: 69  GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAV----ARQALA 124

Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182
           ++G+E L  R P +LSGGQ+QRVA+ RA+   P + L DEPLSNLD ++R+++R EL+ +
Sbjct: 125 LVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDI 184

Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242
             + QAT I VTHDQ EA+++ D++ VM+ G  +QIG P E++  PA+ FVA F+     
Sbjct: 185 LRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ--- 241

Query: 243 NFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPS 302
              N      +G  W    G   + P   E        +  +  +R ED+      L P 
Sbjct: 242 --ANFLATEYQGDAWRTVLG-DFEAPGGLEGSRTG--GEPPVVMVRQEDV-----LLHPH 291

Query: 303 PENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQA 342
           PE   TG+V   + LG +    V++   L +  + P ++A
Sbjct: 292 PEG--TGLVRDRQFLGRDYRYFVQLPAGLEIQVLGPVSEA 329


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: 293
Number of extensions: 10
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: 369
Length of database: 368
Length adjustment: 30
Effective length of query: 339
Effective length of database: 338
Effective search space:   114582
Effective search space used:   114582
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.

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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