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_b21423 SM_b21423 sugar uptake ABC transporter permease

Query= uniprot:D8J112
         (347 letters)



>FitnessBrowser__Smeli:SM_b21423
          Length = 331

 Score =  204 bits (518), Expect = 3e-57
 Identities = 130/344 (37%), Positives = 194/344 (56%), Gaps = 18/344 (5%)

Query: 1   MANNIHSATSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEV 60
           M +N+ S T     +    +   +R    + A    LLAF  L+  I+FFS +SP F+  
Sbjct: 1   MPDNLQSETLPMADLERNRNRAAIRRAPESAA----LLAF--LVAEIIFFSLSSPYFLTW 54

Query: 61  DNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIA 120
            N V++  + ++ GVLA   T ++I    DLSVG+ + F A++  + + + G+ LP  + 
Sbjct: 55  GNWVNVFTALSITGVLAAGGTMLLIAGQFDLSVGSGVAFVALVLALTIDSLGV-LPASVL 113

Query: 121 AAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIA 180
           A +  G   G I+G ++ ++ V   I TLG + + +GL+  I G R I   + +   AI 
Sbjct: 114 AMLV-GVGIGLINGFLVTRIGVNALITTLGTLAIFRGLTQSIGGGRNIPIANFDW--AIW 170

Query: 181 QDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDF 240
           +        P L IP + L+  LVAI   I+L ++VFGR  +A+G+NE A RL G++   
Sbjct: 171 R--------PFLNIPLSALVFLLVAIMVGIVLKRSVFGRSIYAIGANENAARLVGIRTKG 222

Query: 241 WKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGT 300
              A +  SGA  G+ GLI AS+L S     G G EL  + AV++GGTSL GGTGT+LGT
Sbjct: 223 VVFAGFLLSGAFIGLGGLISASQLGSTSGTTGLGLELAVVTAVILGGTSLKGGTGTMLGT 282

Query: 301 IIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344
           +IG  I+ VL NGL +M+V   WQ   TG+++ILAV  D LR+R
Sbjct: 283 VIGLLIVGVLNNGLTLMNVNSSWQQAATGLLLILAVSFDQLRQR 326


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: 247
Number of extensions: 12
Number of successful extensions: 2
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: 331
Length adjustment: 28
Effective length of query: 319
Effective length of database: 303
Effective search space:    96657
Effective search space used:    96657
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