GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Acidovorax sp. GW101-3H11

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_3217 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3217
          Length = 386

 Score =  177 bits (448), Expect = 6e-49
 Identities = 114/367 (31%), Positives = 179/367 (48%), Gaps = 6/367 (1%)

Query: 5   LKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64
           L LT VA  A   G     +  +KIG   P+SG     G+D  NG  +A++ELN  G T+
Sbjct: 14  LALTAVATAAVLTGCGKVPD-TIKIGVAQPLSGPLGALGQDLLNGVTLAVDELNKSGYTV 72

Query: 65  GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124
            GK++  E+V+ DD AD   G A AQ+L DA V  V+GHLNSG +I  + +Y    I  +
Sbjct: 73  DGKRVTLEVVSVDDKADAATGKAVAQQLVDAGVVAVIGHLNSGVSIETAPIYAAKDIAQI 132

Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184
              +TNP  T+ G+ TTFR++ ND      +  +A   L     A +DD T YG+G+AD 
Sbjct: 133 -AISTNPKFTQLGFSTTFRMVGNDTLQARAIGSFAATQLGAARYAALDDGTPYGKGLADG 191

Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244
             +   A+  +VV  +   DK   F  +   +KA   + I     D Q   +L  + ++ 
Sbjct: 192 AAEQLKAEKKEVVVRKSFDDKTVAFDELAGELKAAKVEVIVSTLNDFQALALLEALRKVD 251

Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304
              V   GGD I T+++ K   GA  +  +          +   G  +  KY A Y    
Sbjct: 252 HTKVSLLGGDTIKTTDMTK---GAGIVQGIYATSPVLEAKEFSTGKPFLEKYIAAYKKPP 308

Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPEL-AKSSFKGVTSTIAFEPNGEMKNPAIT 363
                Y+YD+T+++  A+++A S  PK  T  + + + +  V  T+ ++  GE +  A+ 
Sbjct: 309 AYGGHYSYDSTYVLSAAIQKAKSAAPKDITKAMHSINGYAPVIGTMTWDDKGEQRYGAVG 368

Query: 364 LYVYKDG 370
           +Y  + G
Sbjct: 369 VYELRAG 375


Lambda     K      H
   0.315    0.131    0.375 

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: 335
Number of extensions: 17
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: 375
Length of database: 386
Length adjustment: 30
Effective length of query: 345
Effective length of database: 356
Effective search space:   122820
Effective search space used:   122820
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: 50 (23.9 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