GapMind for catabolism of small carbon sources

 

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

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 3608115 Dshi_1520 ABC transporter related (RefSeq)

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Dino:3608115
          Length = 277

 Score =  214 bits (544), Expect = 2e-60
 Identities = 106/231 (45%), Positives = 156/231 (67%)

Query: 5   LVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIF 64
           L+   +  GY +   IL     ++  GE+  ++GPNGAGKST  K +FG+L    G +  
Sbjct: 46  LIGDGMTGGYGSGADILHDCTLAVDRGEIAVIVGPNGAGKSTAMKAVFGMLNIHTGSVRL 105

Query: 65  KGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP 124
            GE+ITGL     V +GM +VPQV N+F ++TV ENL+MGAFL +       +++Y +FP
Sbjct: 106 DGEDITGLSPQARVAKGMAFVPQVNNIFTTMTVEENLEMGAFLRRDDISETMEQVYELFP 165

Query: 125 KLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINA 184
            L ++R Q AG LSGG+RQ +A+GRALM  P +L+LDEP+A +SPI++ ++F +I  +  
Sbjct: 166 ILREKRRQAAGELSGGQRQQVAVGRALMTRPQVLMLDEPTAGVSPIVMDELFDRIIEVAR 225

Query: 185 TGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           TG +I++VEQNA+QAL +AD+GYVL  GR++   +GQ+LL DP V + +LG
Sbjct: 226 TGISILMVEQNARQALEIADKGYVLVQGRNRYTDTGQALLADPDVRKSFLG 276


Lambda     K      H
   0.320    0.139    0.393 

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: 203
Number of extensions: 5
Number of successful extensions: 1
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: 240
Length of database: 277
Length adjustment: 24
Effective length of query: 216
Effective length of database: 253
Effective search space:    54648
Effective search space used:    54648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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