GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC' in Desulfovibrio vulgaris Miyazaki F

Align RnsD, 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 8502320 DvMF_3028 inner-membrane translocator (RefSeq)

Query= TCDB::Q8DU39
         (318 letters)



>FitnessBrowser__Miya:8502320
          Length = 308

 Score =  176 bits (445), Expect = 8e-49
 Identities = 115/321 (35%), Positives = 170/321 (52%), Gaps = 26/321 (8%)

Query: 1   MSLENMLALLISSMLVYA-TPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEF 59
           M ++  L L I +  V + TP++F ++G +F+ERSGV+N+G+EG+M++GAF+G +     
Sbjct: 1   MDMDTALLLSILAATVQSGTPILFATLGEMFTERSGVLNLGVEGMMIVGAFSGFLVT--- 57

Query: 60  AHSFGKATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKAL 119
            H  G   PW   L  GL G   SLLH +  + F+ + +VSG  L +L   LA F     
Sbjct: 58  -HITGN--PWAGVLAAGLCGGGLSLLHGVVCLIFQGNQVVSGLALTILGLGLADFLGTPY 114

Query: 120 YNKGQTDNISQSFGKFDFPILSHIPFLGPIFFQGTSLVAYLAVLFSVFAWFILTKTKFGL 179
                T      F  F  P+L+ IP LG IFF+  +LV YL+ L     W  + +T+ GL
Sbjct: 115 VGITTT-----GFQAFAVPVLADIPVLGAIFFRHDALV-YLSYLLPPLFWLFMARTRPGL 168

Query: 180 RLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFI 239
            LR+ GEHP AA   G++   +R+ G+   G L GIGGA  + + +  +      G G+I
Sbjct: 169 ALRAAGEHPAAASAAGLSPVRIRWCGIFTGGFLAGIGGAYLSLAYTHLWTNNMTSGRGWI 228

Query: 240 ALAAMIFGKWNPIGAMLSSLFFG----LSQSLAVIGGQLPFLSKIPTVYLQIAPYALTIL 295
           A+A +IF  W P  A+  +  FG    L   L  +G  L      P+  + + PYALT+L
Sbjct: 229 AVALVIFAFWRPGRAVFGAYLFGGVMALQLRLQAMGANL------PSSLMLMLPYALTVL 282

Query: 296 VL---AVFFGQAVAPKADGIN 313
           VL   ++  G   AP A G+N
Sbjct: 283 VLLASSLRGGGRAAPAALGVN 303


Lambda     K      H
   0.328    0.143    0.422 

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: 284
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: 318
Length of database: 308
Length adjustment: 27
Effective length of query: 291
Effective length of database: 281
Effective search space:    81771
Effective search space used:    81771
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: 48 (23.1 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