GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Cupriavidus basilensis 4G11

Align ABC transporter permease (characterized, see rationale)
to candidate RR42_RS14420 RR42_RS14420 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Cup4G11:RR42_RS14420
          Length = 308

 Score =  255 bits (651), Expect = 1e-72
 Identities = 137/302 (45%), Positives = 198/302 (65%), Gaps = 13/302 (4%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65
           QQ++NGL LG++YALIA+GYTMVYGII +INFAHGE+ MIGA      +  + GA  G P
Sbjct: 10  QQLVNGLTLGAIYALIAIGYTMVYGIIGMINFAHGEIYMIGAYVGLVTLTAI-GASAGYP 68

Query: 66  GWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKP 125
             ++L  A +++ +V     F +E+VAYRPLR  PRL PLI+AIGMSI LQ    I    
Sbjct: 69  LPLVLGAALLVSVLVTGLYGFAVERVAYRPLRGGPRLVPLISAIGMSIFLQNYVQIGQGA 128

Query: 126 NYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181
                P ++  +  F++G  F   +  +++LI+GVT V + +L   + H+ +GRA RA A
Sbjct: 129 RDMSVPVLISGAIEFQMGSDFTVTVPYSRLLIVGVTLVLMLALTLFIGHSRMGRACRACA 188

Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241
           E+ R+A+L+G+  + VIS TF++GA+LAA+ G++     G     +GF+ G+KAFTAAV 
Sbjct: 189 EDMRMANLLGIDTNRVISFTFVLGAMLAAVGGVLIGLTIGKLNPYIGFVAGIKAFTAAVL 248

Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLL 301
           GGIG++ GA++GG+LLGL E   SGY        + + Y D+ AF +L++IL  RP+GLL
Sbjct: 249 GGIGSIPGAMLGGVLLGLAETFASGY--------MPAEYKDVVAFGLLVLILLFRPTGLL 300

Query: 302 GE 303
           G+
Sbjct: 301 GK 302


Lambda     K      H
   0.327    0.142    0.419 

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: 278
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: 309
Length of database: 308
Length adjustment: 27
Effective length of query: 282
Effective length of database: 281
Effective search space:    79242
Effective search space used:    79242
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 (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