GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livJ in Pseudomonas fluorescens FW300-N1B4

Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate Pf1N1B4_1382 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= TCDB::P0AD96
         (367 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1382 Branched-chain amino
           acid ABC transporter, amino acid-binding protein (TC
           3.A.1.4.1)
          Length = 377

 Score =  285 bits (730), Expect = 1e-81
 Identities = 153/362 (42%), Positives = 219/362 (60%), Gaps = 7/362 (1%)

Query: 6   KALLAGCIALAFSNMALAE-DIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKG 64
           K  LA  +A A    A A+ DIK+ V G M+G  A +G+Q   GA+ A   +NA GG+ G
Sbjct: 8   KGFLALAVATALGVSAFAQADIKIGVAGPMTGANAAFGEQYMKGAQAAADAVNAAGGVNG 67

Query: 65  NKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAA 124
            K+ +VK DDAC+PKQAV VA  + N  +  V+GH CSSST PAS+IY++ GI+ ITP +
Sbjct: 68  EKIVLVKGDDACEPKQAVTVAKDLTNQKVAGVVGHFCSSSTIPASEIYDEAGIIAITPGS 127

Query: 125 TAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDG 184
           T P +T RG   + R  G D  QG  A  YI++ +K +++ ++HDK  YG+GLA A +  
Sbjct: 128 TNPAVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVVVLHDKDTYGQGLADATKAQ 187

Query: 185 LKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK-T 243
           L K     V ++G+T GEKDFST+V +++    D VY+GG HPE G ++RQ R  GLK  
Sbjct: 188 LAKRGVTPVLYEGLTRGEKDFSTIVTKIRGAGADVVYFGGLHPEAGPLVRQLREQGLKDV 247

Query: 244 QFMGPEGVANVSLSNIAG--ESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFVW 301
           +FM  +G+    L   AG  +  +G+L+T   +   +P +K +VD  + K  +P G +  
Sbjct: 248 KFMSDDGIVTDELVTTAGGPQFVDGVLMTFGADPRLLPDSKTVVDDFRKKGTEPEG-YTL 306

Query: 302 TTYAALQSLQAGLN--QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHA 359
             YA++Q+L A  N  +S+   E A +LK N V TVMG  TWD KGDLK  ++ V+ W  
Sbjct: 307 YAYASVQTLAAAFNGAKSNKGEEAAAWLKKNPVKTVMGEKTWDSKGDLKISDYVVYQWDK 366

Query: 360 NG 361
           +G
Sbjct: 367 DG 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: 426
Number of extensions: 25
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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