GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05255 in Sinorhizobium meliloti 1021

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__Smeli:SM_b21375
          Length = 320

 Score =  216 bits (551), Expect = 5e-61
 Identities = 122/308 (39%), Positives = 194/308 (62%), Gaps = 11/308 (3%)

Query: 40  FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99
           F SL+++ + FSF +P FM V N ++ILQ  AV  + A   T+VI+   IDLSVG+++  
Sbjct: 22  FLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTWVILLGEIDLSVGSIIAV 81

Query: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGL- 158
            A M G     +GM     IA  +  GAL G ++G++ AKL +P FI T+  M + +G+ 
Sbjct: 82  -AGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLPSFIVTVATMGIYRGMV 140

Query: 159 SLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFG 218
           SL  +G   +  N+T  ++AI  +S +G       +P  + ++ ++ +   I+L+KT FG
Sbjct: 141 SLPTNGAPAMIENET--WTAIGTESFLG-------LPIIIWVVAVLFVINQIVLSKTSFG 191

Query: 219 RYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELD 278
           R  +  G N EA   SG+KVD  K+ ++  SG +  I+G++++SRL SAQ   G  YELD
Sbjct: 192 RRAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQTNAGMSYELD 251

Query: 279 AIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYL 338
           AIAA V+GGTSL+GG GT++GT+IGA I+ V+ NG+ ++SV   +Q +V G++I++AV+L
Sbjct: 252 AIAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKGLVILVAVWL 311

Query: 339 DILRRRRR 346
           D+  ++ +
Sbjct: 312 DVRAKQAK 319


Lambda     K      H
   0.326    0.139    0.398 

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: 286
Number of extensions: 12
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: 347
Length of database: 320
Length adjustment: 28
Effective length of query: 319
Effective length of database: 292
Effective search space:    93148
Effective search space used:    93148
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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