GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupB in Azospirillum brasilense Sp245

Align RnsC, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate AZOBR_RS06955 AZOBR_RS06955 sugar ABC transporter permease

Query= TCDB::Q8DU38
         (358 letters)



>FitnessBrowser__azobra:AZOBR_RS06955
          Length = 362

 Score =  177 bits (448), Expect = 5e-49
 Identities = 104/337 (30%), Positives = 176/337 (52%), Gaps = 10/337 (2%)

Query: 11  PLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIALGFAV 70
           PL++V L +  G ++    G+DP+ A    F     SL+ +GE+    +PL+L A+G A+
Sbjct: 21  PLLAVALTLASGFLLFWAMGFDPVKALHAFFIAPLLSLRGLGELAVKATPLVLCAIGLAI 80

Query: 71  ASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGGVVGAIPGFLR 130
             RA  +NIG  GQ   G I  G  ALA        ++ + ++ G A G +  AIP FLR
Sbjct: 81  GFRANVWNIGAEGQLTLGAITGGGLALAFYGEGGWWLLPLMIVAGMAGGALWAAIPAFLR 140

Query: 131 AYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASYQTEWLRALTN 190
                SE++ ++M+NY+ L++ N ++   +     R+ D   +           L  L  
Sbjct: 141 VRFNASEILTSLMLNYVALHLLNYLMHGPY-----RDPDGFAFPESRLFEADAVLPLLVA 195

Query: 191 NSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTIVLSMIISG 250
            +R+++G   A++A+   W+L+ +T +GF+I+ +GL P A+ YAG + K+ I L++++SG
Sbjct: 196 GTRVHLGSLFALLAVAAGWFLMARTFIGFQIKVIGLTPTAAGYAGFNQKKIIWLTLLLSG 255

Query: 251 ALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLFGALSVGAP 310
           ALAGL G+ E  G  G +   T S   G+  + V+ L    P+GI L+ FL     +G  
Sbjct: 256 ALAGLAGLGEVAGPIGQMN-PTISPGYGYTAIIVAFLGRLHPVGILLAGFLMALSFIGGE 314

Query: 311 GMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHY 347
              I+    +G P  +  V   +++FF+ A  ++  Y
Sbjct: 315 AAQIA----LGLPKAITGVFQGMLLFFLLATDVLIRY 347


Lambda     K      H
   0.325    0.141    0.416 

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: 362
Number of extensions: 24
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: 362
Length adjustment: 29
Effective length of query: 329
Effective length of database: 333
Effective search space:   109557
Effective search space used:   109557
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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