GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Desulfovibrio vulgaris Miyazaki F

Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)

Query= TCDB::Q8YXD0
         (288 letters)



>FitnessBrowser__Miya:8501893
          Length = 302

 Score =  136 bits (343), Expect = 5e-37
 Identities = 83/288 (28%), Positives = 158/288 (54%), Gaps = 13/288 (4%)

Query: 7   QLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFV-NTFGVN----- 60
           +L   G+  GSI AL A+G T+ YGI+ L NFAHG+   +GA+    V    G+      
Sbjct: 8   ELFFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGALGIYGFPAL 67

Query: 61  --IWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGG 118
             + ++ +VAV+      L  EK+ +  +R   A   + +I +IG+++FL+N +IL    
Sbjct: 68  AILIIAAVVAVIYCAAYGLTLEKIAYKPLRD--APRLSPLISAIGMSIFLQNYVILAQTS 125

Query: 119 RNQNYN--LPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDL 176
               +   +P    L+     +  +++L++  + +S+ AL   ++ T++GKAMRA A + 
Sbjct: 126 DFMPFPNLVPQPDFLEPIAHIMGASEVLIIVTSAISMAALTLFIKYTRMGKAMRATAQNR 185

Query: 177 DLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGL-ITAVRPNMGWFLILPLFASVILGGI 235
            +A + GID ++VI  T++I  ++ ++GG +    +  V   +G+   +  F + +LGGI
Sbjct: 186 KMAMLLGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAFTAAVLGGI 245

Query: 236 GNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283
           G+  GA+    ++G  +  +T ++ S Y+  +A  +++L+L+ RP G+
Sbjct: 246 GSIPGAMLGGLVLGWCESFATGYISSDYEDALAFALLVLILIFRPSGI 293


Lambda     K      H
   0.328    0.144    0.426 

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: 222
Number of extensions: 18
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: 288
Length of database: 302
Length adjustment: 26
Effective length of query: 262
Effective length of database: 276
Effective search space:    72312
Effective search space used:    72312
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