GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Pseudomonas fluorescens FW300-N2E3

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO353_17120 AO353_17120 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17120
          Length = 307

 Score =  142 bits (359), Expect = 7e-39
 Identities = 89/294 (30%), Positives = 161/294 (54%), Gaps = 21/294 (7%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS----GIN-L 59
           Q + NG+ +GS  AL A+G T+ YGI+ + NFAHG+   + +Y+ +         GI+ L
Sbjct: 9   QQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIVLAGLAMLGIHSL 68

Query: 60  WLSMALGCVGTIIAM----FIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWG 115
            L M    + TI+      +  E + ++P+R         +I +IG+++FL+N +LL   
Sbjct: 69  PLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIP--LISAIGMSIFLQNTVLL--S 124

Query: 116 GNNQNYRVP-IVPAQDFMG------IKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168
            ++++  +P ++P     G      +   Y ++LV  + +  M+ L   + R+++G+A R
Sbjct: 125 QDSKDKSIPNLIPGSFSFGPGGAQEVLISYMQILVFVVTLVVMLCLTTFISRSRLGRACR 184

Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMT-TLKPNMGWFLILPMFAS 227
           A A+++ +A + GIN   ++  T+V+ A L A+   +  +    + PN G+ + L  F +
Sbjct: 185 ACAEDIRMANLLGINTNNIIALTFVIGAALAAVAAVLLSMQYGVINPNAGFLVGLKAFTA 244

Query: 228 VILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
            +LGGIG+  GA+ GG+++GVA+      FG  YK  VA  L++++L  RP GL
Sbjct: 245 AVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGL 298


Lambda     K      H
   0.329    0.143    0.450 

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: 180
Number of extensions: 7
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: 286
Length of database: 307
Length adjustment: 26
Effective length of query: 260
Effective length of database: 281
Effective search space:    73060
Effective search space used:    73060
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 (21.8 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