GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1382
          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.

Links

Downloads

Related tools

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