GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Dinoroseobacter shibae DFL-12

Align NatE, 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 3610347 Dshi_3728 ABC transporter related (RefSeq)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Dino:3610347
          Length = 236

 Score =  170 bits (431), Expect = 2e-47
 Identities = 88/217 (40%), Positives = 136/217 (62%), Gaps = 2/217 (0%)

Query: 10  PLLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKI 69
           P+L +EN+H+ Y     ++QGV+  V  GE++ V G NG GK+TL K I G + P +G I
Sbjct: 4   PMLSIENLHSHYGLS-HVIQGVSLDVGRGEILGVFGRNGVGKTTLLKNIAGWVKPSSGSI 62

Query: 70  TFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAF-IRNDSLQPLKDKIFA 128
              GK I G + + I R G+  VP+   +FP L+V+ENLE+G   ++    +   D +  
Sbjct: 63  RMDGKQIGGDEPDAINRAGLAIVPEDRRIFPGLTVQENLELGLLGLKGPKPRSKLDPVLE 122

Query: 129 MFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQ 188
            FPRL++R +Q A TLSGGE+QMLAM + ++ EP  +++DEPS  L+P++V ++F  +++
Sbjct: 123 RFPRLAERAQQPATTLSGGEQQMLAMARIMVAEPRAVLIDEPSEGLAPMIVAEIFAILRE 182

Query: 189 INQEGTAIILVEQNARKALEMADRGYVLESGRDAISG 225
           +   G AI+LVEQN  +AL + DR  ++E G     G
Sbjct: 183 MKDAGCAIVLVEQNIHEALSICDRFVLVERGAIVFEG 219


Lambda     K      H
   0.317    0.136    0.377 

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: 181
Number of extensions: 11
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: 247
Length of database: 236
Length adjustment: 23
Effective length of query: 224
Effective length of database: 213
Effective search space:    47712
Effective search space used:    47712
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 (21.6 bits)
S2: 46 (22.3 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