GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Dechlorosoma suillum PS

Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate Dsui_2061 Dsui_2061 ABC-type branched-chain amino acid transport system, periplasmic component

Query= uniprot:D8IUY1
         (378 letters)



>lcl|FitnessBrowser__PS:Dsui_2061 Dsui_2061 ABC-type branched-chain
           amino acid transport system, periplasmic component
          Length = 384

 Score =  121 bits (304), Expect = 3e-32
 Identities = 109/356 (30%), Positives = 162/356 (45%), Gaps = 19/356 (5%)

Query: 8   LNIIAASLALIPAFAMAQETQV--VKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPI 65
           +  +  SL L+ A A A   Q   +KIG ++ LTG  A  G   + G  +A + +NA+  
Sbjct: 1   MRFLPKSLVLVGALAAAGLAQAADIKIGVAAALTGGAAQYGVAIRNGFQLAADEINAKG- 59

Query: 66  TVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQG-VKAIVGPYNSGVTIPASRVYNDAGI 124
            V G KI+  ++ ED+Q   + G+ V +KL  Q  V  + GP  S     A  V N A  
Sbjct: 60  GVNGNKIQ--LVVEDEQGKKEEGINVFKKLIFQDKVLMVFGPTLSNSMFAAGPVANGAKT 117

Query: 125 VV-ATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVI---DDRTAYG 180
           VV  T  +   IT  G   +FR +  +S +       A K  K K+VAVI   DD  A+ 
Sbjct: 118 VVFGTSVTANGITDIG-PYVFRNSVMESDVLPVTVATATKHYKLKQVAVIYGNDD--AFT 174

Query: 181 QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR 240
           +     F KV +   + V +T+       DF A LT IK   PDAV     A +   I  
Sbjct: 175 KSGYDVFKKVLEDQKLPVTTTETYVKGDVDFKAQLTKIKASNPDAVICSCLAEEAANIML 234

Query: 241 QMKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKY 300
           Q + LG+ VP +GG+G  SP++  +   A GE  +     +  + A   K F   Y KKY
Sbjct: 235 QARGLGIKVPFIGGNGFNSPKLFEISKLA-GEGTFVGSPWSNTNPAPANKAFVAAYVKKY 293

Query: 301 NRPAETYAVSFYDGMMLIAQAMKQAN-----SVDPKQFGPALAKISYKGVAGQYDF 351
           N     +A   +D + + A A+++       + D +    AL K +  G  G + F
Sbjct: 294 NAEPNQFAAQAFDALHVAAAALQEVKLSGDIAADREALKNALPKATINGATGPFKF 349


Lambda     K      H
   0.316    0.134    0.378 

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: 423
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: 378
Length of database: 384
Length adjustment: 30
Effective length of query: 348
Effective length of database: 354
Effective search space:   123192
Effective search space used:   123192
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: 41 (21.6 bits)
S2: 50 (23.9 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 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