GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SynE:Synpcc7942_1406 Synpcc7942_1406 ATPase
          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 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