GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Acidovorax sp. GW101-3H11

Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate Ac3H11_1432 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:A0A0D9B2B6
         (307 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1432 High-affinity
           branched-chain amino acid transport system permease
           protein LivH (TC 3.A.1.4.1)
          Length = 294

 Score =  137 bits (345), Expect = 3e-37
 Identities = 90/294 (30%), Positives = 158/294 (53%), Gaps = 17/294 (5%)

Query: 10  QLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGLAMMGLDSVP 69
           QL+ GL  GS YA++++G  +++G++ +INFAHG ++M G+ + ++A   +  +G++   
Sbjct: 14  QLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMTGALITWMA---MNYLGINYWL 70

Query: 70  LLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTV--LLSQDS 127
           +L+ A  +  +     +G  IER+  R +   + L  L+  +G+++ ++     +     
Sbjct: 71  MLVLAPLVVGL-----FGVLIERLLLRWIYKLDHLYGLLLTLGLTLLIEGVFRSIYGVSG 125

Query: 128 KDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLGRACRACA 187
                P L+ G   +G      ++ +Y   VV V ++V  +     I +++LG   RA  
Sbjct: 126 LGYDTPELLEGATNLG----FMIMPNYRAWVV-VASIVVCVATWYVIEKTKLGAYLRAGT 180

Query: 188 EDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLKAFTAAVL 247
           E+ ++    GIN   ++ LT+  GAALAA A VL +  Y V  P  G  + +  F   V+
Sbjct: 181 ENPRLVEAFGINVPVMVTLTYAFGAALAAFAGVLAAPVYQV-TPLMGQNLIIVVFAVVVI 239

Query: 248 GGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGR 301
           GG+GSI G++L GL LGV E F   +F  +    V F ++V+VLL RP G+ G+
Sbjct: 240 GGMGSIMGSILTGLGLGVIEGF-TKVFYPEASSTVVFVIMVIVLLIRPAGLFGK 292


Lambda     K      H
   0.327    0.144    0.411 

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: 273
Number of extensions: 14
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: 307
Length of database: 294
Length adjustment: 27
Effective length of query: 280
Effective length of database: 267
Effective search space:    74760
Effective search space used:    74760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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