GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Rhizobium etli CFN 42

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_042119961.1 RHE_RS26930 carbohydrate ABC transporter permease

Query= reanno::psRCH2:GFF851
         (296 letters)



>NCBI__GCF_000092045.1:WP_042119961.1
          Length = 271

 Score =  115 bits (287), Expect = 1e-30
 Identities = 71/213 (33%), Positives = 118/213 (55%), Gaps = 9/213 (4%)

Query: 83  LWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSLVAIYA 142
           L+LWNS+ +   +++L L++   + Y  AR++    A I+   +I +M P +  L+ ++ 
Sbjct: 68  LYLWNSLLVTGAATLLALVIGVPAGYGIARLKAEKSAMII---MIARMTPGLSFLIPLFL 124

Query: 143 LFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGATTWQA 202
           LF    Q ++ LG      +I+  +  + + +W + GYFE+    LEEAA +DGAT WQ 
Sbjct: 125 LF----QWLNLLGTLMP-QIIIHLVVTVPIVVWIMIGYFETTPMELEEAASIDGATPWQV 179

Query: 203 FFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYLYPQNYLWGD 262
           F  + LP++ P + V FIL+ I S   + +  ++L   +  TL V     L  +   WG 
Sbjct: 180 FRLVALPIARPGIVVAFILSVIFSWNNF-VFGIVLASRETRTLPVAVYNMLSFEQVSWGP 238

Query: 263 FAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295
            AAAA++  LP+  + ++ Q+ IV GLTAG VK
Sbjct: 239 LAAAALIVTLPVLILTVFAQRQIVAGLTAGAVK 271


Lambda     K      H
   0.327    0.139    0.433 

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: 243
Number of extensions: 15
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: 296
Length of database: 271
Length adjustment: 26
Effective length of query: 270
Effective length of database: 245
Effective search space:    66150
Effective search space used:    66150
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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