GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Pseudomonas fluorescens FW300-N2C3

Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AO356_08500 AO356_08500 amino acid ABC transporter substrate-binding protein

Query= TCDB::P0AD96
         (367 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08500
          Length = 378

 Score =  279 bits (713), Expect = 1e-79
 Identities = 150/363 (41%), Positives = 222/363 (61%), Gaps = 8/363 (2%)

Query: 6   KALLAGCIALAFSNMALAE-DIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKG 64
           K  LA  +A A    A A+ D+K  V G M+G  A +G+Q   GA+ A   IN  GG+ G
Sbjct: 8   KGFLALAVAAALGVSAFAQADVKFGVAGPMTGANAAFGEQYMKGAQAAADAINKAGGVNG 67

Query: 65  NKLQIVKYDDACDPKQAVAVANKVVN-DGIKYVIGHLCSSSTQPASDIYEDEGILMITPA 123
            K+ +V  DDAC+PKQAVAVAN++V+ D +  V+GH CSS+T PAS++Y++ GI+ ITP 
Sbjct: 68  EKIVLVAGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGIIAITPG 127

Query: 124 ATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQD 183
           +T P++T RG   + R  G D  QG  A  YI++ +K +++A++HDK  YG+GLA A + 
Sbjct: 128 STNPQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADATKA 187

Query: 184 GLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK- 242
            L K     V ++G+T GEKDFS +V +++    D VY+GG HPE G ++RQ R  GLK 
Sbjct: 188 QLAKRGVKEVLYEGLTRGEKDFSAVVTKIRSVGADVVYFGGLHPEAGPLVRQLREQGLKD 247

Query: 243 TQFMGPEGVANVSLSNIAG--ESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300
            +FM  +G+    L   AG  +  +G+ +T   +   +P +K +V+  +    +P G + 
Sbjct: 248 VKFMSDDGIVTDELVTTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKNGTEPEG-YT 306

Query: 301 WTTYAALQSLQAGLN--QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH 358
              YA++Q+L AG N  +S+   + AK+LKAN V TVMG   WD KGDLK  ++ V+ W 
Sbjct: 307 LYAYASVQALAAGFNGAKSNKGEDAAKWLKANPVQTVMGKKEWDTKGDLKVSDYVVYQWD 366

Query: 359 ANG 361
            +G
Sbjct: 367 KDG 369


Lambda     K      H
   0.314    0.133    0.380 

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: 428
Number of extensions: 23
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: 367
Length of database: 378
Length adjustment: 30
Effective length of query: 337
Effective length of database: 348
Effective search space:   117276
Effective search space used:   117276
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: 42 (22.0 bits)
S2: 50 (23.9 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