GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Sinorhizobium meliloti 1021

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc02378 SMc02378 periplasmic binding transmembrane protein

Query= TCDB::Q9KKE3
         (346 letters)



>FitnessBrowser__Smeli:SMc02378
          Length = 332

 Score =  175 bits (443), Expect = 2e-48
 Identities = 118/343 (34%), Positives = 177/343 (51%), Gaps = 26/343 (7%)

Query: 11  TFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIP 70
           T  AAGL+   SA  A+A+ CGD   VT A ++W+S   +  V K IL++GY C  + + 
Sbjct: 8   TCLAAGLLGLGSA--ASAAECGD---VTIANMNWQSAEVLASVDKFILTEGYGCSAELVV 62

Query: 71  GNSV-TLEQATANNDVQIFAEEWLGR-SDVWNKAVEEKKVIAVGKTFV-GASEGWFVPDY 127
           G++V T+       +  I  E W+    DV N+ ++E K++        GA +GW+VP Y
Sbjct: 63  GDTVPTITSMIEKGEPDIAPEGWVDLLPDVVNRGLQEGKLVGAAVALSDGAVQGWWVPKY 122

Query: 128 VVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKL 187
           +V  +P         D+K++  +   K  E+F DPE+PSKG   N P GW    V+T   
Sbjct: 123 IVDANP---------DIKTIDDVLKHK--ELFPDPEDPSKGAIFNGPQGWGGTVVTTQLY 171

Query: 188 EAY---KLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPA 244
           +AY     G T V+   G+   LD +I  AY + +    YYW+PTA+LGK+++++LE   
Sbjct: 172 KAYGAEAAGFTLVD--TGSAAGLDGSIAKAYERKQGWAGYYWAPTALLGKYEMVKLEHGV 229

Query: 245 YNE-ACWKELSSANGKRD-EGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 302
            N+ A WK  ++     D +   +P   V   V   FA  A   +E L    +  D VN 
Sbjct: 230 PNDMAEWKRCNTVADCPDPKKNDWPKDKVQTLVTKEFADRAGPAMEYLNTRAWTNDTVNK 289

Query: 303 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345
            +A+M DN+      A  FL+   D+W+KWVS E   KI+A L
Sbjct: 290 LMAWMTDNQASGEEGAKHFLEENPDLWTKWVSPEVAEKIKAAL 332


Lambda     K      H
   0.314    0.130    0.391 

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: 354
Number of extensions: 18
Number of successful extensions: 5
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: 346
Length of database: 332
Length adjustment: 28
Effective length of query: 318
Effective length of database: 304
Effective search space:    96672
Effective search space used:    96672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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