GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacK in Sinorhizobium meliloti 1021

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate SM_b20630 SM_b20630 sugar uptake ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>lcl|FitnessBrowser__Smeli:SM_b20630 SM_b20630 sugar uptake ABC
           transporter ATP-binding protein
          Length = 361

 Score =  383 bits (984), Expect = e-111
 Identities = 207/360 (57%), Positives = 257/360 (71%), Gaps = 18/360 (5%)

Query: 6   LSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTIDDV 65
           LSD+RKSYGGLEVI G+DL I+ G+FVVFVGPSGCGKSTLLRMIAGLEE+S G++ I   
Sbjct: 12  LSDIRKSYGGLEVIHGIDLTIEEGDFVVFVGPSGCGKSTLLRMIAGLEEVSEGEIAIKGR 71

Query: 66  RMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGA 125
            + D+DPS+RGIAMVFQSYALYPHM+V EN+GF L+ A    AEI +RV + + IL++  
Sbjct: 72  DVTDLDPSERGIAMVFQSYALYPHMSVSENLGFGLKMARTDPAEIARRVAQVSAILKIDH 131

Query: 126 LLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLAT 185
           LLDR+P QLSGGQRQRVAIGRAIVR P +FLFDEPLSNLDAELRV MRIEIARLH++L  
Sbjct: 132 LLDRRPGQLSGGQRQRVAIGRAIVRKPDVFLFDEPLSNLDAELRVSMRIEIARLHRELGN 191

Query: 186 TIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMNFL--- 242
           T+VYVTHDQ EAMTLAD+IVV+R G +EQ GSP D+Y+DPAN+FVAGFIGSP+MNFL   
Sbjct: 192 TMVYVTHDQTEAMTLADQIVVLRDGRIEQAGSPRDVYEDPANMFVAGFIGSPRMNFLDAE 251

Query: 243 ---KGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHF--DEAGPAALDLA 297
               G I + E    A + D G  K         G  + +GIRPEH    E GP  +   
Sbjct: 252 WQGDGTIRVGETTLEAAI-DGGSLK--------HGERLLLGIRPEHIAVAEPGPERIAAQ 302

Query: 298 IDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGEGKRLR 357
           ++  E+LGG  + Y +   +G+ +VVE + G   + G++L+          F  +G+RLR
Sbjct: 303 VEFSEYLGGTRYLYCQLE-DGQSLVVEQREGPNWQAGEKLSFAVPDDRRRFFAEDGRRLR 361


Lambda     K      H
   0.321    0.139    0.396 

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: 418
Number of extensions: 22
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: 358
Length of database: 361
Length adjustment: 29
Effective length of query: 329
Effective length of database: 332
Effective search space:   109228
Effective search space used:   109228
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 paper from 2022 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