GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Erythrobacter marinus HWDM-33

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_082126415.1 AAV99_RS08705 phosphate ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_001013305.1:WP_082126415.1
          Length = 283

 Score =  142 bits (357), Expect = 9e-39
 Identities = 87/245 (35%), Positives = 136/245 (55%), Gaps = 12/245 (4%)

Query: 2   IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEK--PNG---G 56
           ++   +S  +G  + +  +S  +    V A IGPSG GKSTFLR LN +    P+    G
Sbjct: 36  MRARDVSVYYGNKKAIDEVSVDVFSEYVTAFIGPSGCGKSTFLRALNRMNDTIPSARVEG 95

Query: 57  TITIKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAP-VNVKKESKQAAQE 115
           TI +   +I     + +++R  +GMVFQ  + FP K++ +N+ Y P ++   E K     
Sbjct: 96  TIELDGEDIYSSGMDVVQLRARVGMVFQKPNPFP-KSIYDNVAYGPKIHGLAEGKTELDA 154

Query: 116 KAEDLLRKVGLFE----KRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEM 171
             E  L + GL+E    +  D    LSGGQ+QR+ IARA+A++P+++L DEP SALDP  
Sbjct: 155 IVEKSLTRAGLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIA 214

Query: 172 VKEVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKR 231
              + +++ +L      +VIVTH M  A  V+ R  F   G +VE G+  + F +PK +R
Sbjct: 215 TARIEELIDDL-RGRYAIVIVTHSMQQAARVSQRTAFFHLGHLVEYGHTSDIFTNPKQQR 273

Query: 232 AQDFL 236
            QD++
Sbjct: 274 TQDYI 278


Lambda     K      H
   0.317    0.134    0.368 

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: 166
Number of extensions: 13
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: 240
Length of database: 283
Length adjustment: 25
Effective length of query: 215
Effective length of database: 258
Effective search space:    55470
Effective search space used:    55470
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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