GapMind for catabolism of small carbon sources

 

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

Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein

Query= TCDB::P0AD96
         (367 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13340
          Length = 377

 Score =  286 bits (731), Expect = 8e-82
 Identities = 155/363 (42%), Positives = 221/363 (60%), Gaps = 7/363 (1%)

Query: 4   KGKALLAGCIALAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIK 63
           KG   LA   AL  S+   A D+K+ V G M+GP A +G Q   GA+ A   INAKGGI 
Sbjct: 8   KGFVALAVAAALGVSSFVQA-DVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGIN 66

Query: 64  GNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPA 123
           G K+ +V+ DDAC+PKQAVAVANK+V D +  V+GH CSSST PAS++Y D GI+ ITP 
Sbjct: 67  GEKIVLVQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPG 126

Query: 124 ATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQD 183
           +T P +T RG   ++R  G D  QG  A  YI++ +K +++A+++DK  YG+GLA A   
Sbjct: 127 STNPTVTERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAK 186

Query: 184 GLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK- 242
            L       V  +G+T GEKDFS L+ +++    D +Y+GG HPE G ++ Q R  GLK 
Sbjct: 187 QLTARGVKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKD 246

Query: 243 TQFMGPEGVANVSLSNIAGES--AEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300
            +FM  +G+    +   AG +   +G+ +T   +   +P +K +VD  +    +P G + 
Sbjct: 247 VKFMSDDGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEG-YT 305

Query: 301 WTTYAALQSLQAGLN--QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH 358
              YA++Q+L AG N  +S+   E AK+LKA+ V+TVMG   WD KGDLK  ++ V+ W 
Sbjct: 306 LYAYASVQALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQWD 365

Query: 359 ANG 361
           A G
Sbjct: 366 AAG 368


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: 434
Number of extensions: 23
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: 367
Length of database: 377
Length adjustment: 30
Effective length of query: 337
Effective length of database: 347
Effective search space:   116939
Effective search space used:   116939
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: 49 (23.5 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