GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylE_Tm in Sinorhizobium meliloti 1021

Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate SMc03813 SMc03813 periplasmic binding ABC transporter protein

Query= uniprot:Q9WXW9
         (335 letters)



>FitnessBrowser__Smeli:SMc03813
          Length = 337

 Score =  114 bits (284), Expect = 5e-30
 Identities = 106/342 (30%), Positives = 151/342 (44%), Gaps = 54/342 (15%)

Query: 13  MRKLLVFLSVL-LVAGLS----------LALTIGVIGKSVHPYWSQVEQGVKAAGKALG- 60
           +R L   LSV  L AGL+           AL   V+  +  P    ++QG +AA K LG 
Sbjct: 4   VRTLTAALSVACLAAGLTAPQANAADREFALVFKVLNNAFSP---PIQQGCEAAAKKLGD 60

Query: 61  VDTKFFVPQKEDINAQLQMLESFIAEGVNGIAIAPSDPTAVIPTIKKALEMGIPVVTLDT 120
           V   +  P + D   Q+Q+ +  +  GV G+ ++  +P A+   +K A + GIPVVT DT
Sbjct: 61  VTCTYLGPTEYDEAKQVQLAQDMVTRGVAGLGVSAGNPKAMARIMKMAQDKGIPVVTFDT 120

Query: 121 D--SPDSG-RYVYIGTDNYQAGYTAGLIMKELLGGKGKVVIGTGSLTAMNSLQRIQGFKD 177
           D    D+G R  YIGTDNY+ G      + E     G V I +G+  + N   R+QG +D
Sbjct: 121 DVLPEDAGLRSTYIGTDNYEFGIALAQKVLESKKDGGTVCIQSGAPASENLKARVQGIRD 180

Query: 178 AI----KDSEIEIVDILN-----------DEEDGARAVSLAEAALNAHPDLDAFFGV--- 219
            +    KD   E +   N           + +D   A       +  +P+L AF  V   
Sbjct: 181 TLAGVTKDKGAEKLTGQNGWTEPAGCPVYNNDDITLAAQQVRDVMTNNPELSAFVAVGGW 240

Query: 220 --YAYNGPAQALVVKNAGKVGKVKIVCF-DTTPDILQYVKEGVIQATMGQRPYMMGYLSV 276
             YA     QA+    A    K  +V F D     L  + EG+    +GQRPY MGY   
Sbjct: 241 AQYAPQAYKQAMEPLKARLDSKDLVVVFGDNFGPQLPLLAEGLSHYNIGQRPYDMGY--- 297

Query: 277 TVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPEN 318
                        T+M L K+    KV+  I TG +V TPE+
Sbjct: 298 ------------ETIMALDKLTKGEKVEPFIKTGTEVCTPED 327


Lambda     K      H
   0.318    0.137    0.388 

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: 228
Number of extensions: 11
Number of successful extensions: 4
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: 335
Length of database: 337
Length adjustment: 28
Effective length of query: 307
Effective length of database: 309
Effective search space:    94863
Effective search space used:    94863
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: 41 (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