GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Herbaspirillum seropedicae SmR1

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate HSERO_RS16730 HSERO_RS16730 sugar ABC transporter permease

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



>FitnessBrowser__HerbieS:HSERO_RS16730
          Length = 293

 Score =  115 bits (289), Expect = 9e-31
 Identities = 88/291 (30%), Positives = 137/291 (47%), Gaps = 27/291 (9%)

Query: 12  RLWAT-HAALLAFVAAILFPLLMVISISFREGN---FATGSLF-PENPTLEHWSLALGIP 66
           R W T +  LL F+  +LFP   ++  +F+  N     +G+ F    PTL H+   L   
Sbjct: 22  RKWVTIYIPLLIFLFVLLFPFYWMVITAFKPDNELLSQSGNPFWVIAPTLAHFKKLL--- 78

Query: 67  YTHADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSML 126
                   TQ P     WL N+V ++ VS+   L  S  +AYA  R+RF G   +   + 
Sbjct: 79  ------FDTQYP----AWLLNTVIVSVVSTFASLAASVFAAYAIERLRFQGSKQVGLGIF 128

Query: 127 IFQMFPPVLSLVAIYALFDQLGQH-VSWLGVNSHGAVIVASLGGMALHIWTIKGYFESID 185
           +  + PP +  + + A+  +LG     W  + ++   ++          W + GYF SI 
Sbjct: 129 LAYLIPPSILFIPLAAIVFKLGLFDTRWALILTYPTFLIPFC------TWLLMGYFRSIP 182

Query: 186 ASLEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTL 245
             LEE A++DGAT W+    I+LP++VP L    I AF  S  E+  A   +   +  T+
Sbjct: 183 YELEECALIDGATRWEILVKIILPLAVPGLISAGIFAFTLSWNEFIYALTFISSSEVKTV 242

Query: 246 SVGAQQYLYPQN-YLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295
            VG    L   + Y WG   A A+L  LP+  V+ +  ++ V G+T G VK
Sbjct: 243 PVGIVTELVEGDVYHWGALMAGALLGSLPVAVVYSFFVEYYVSGMT-GAVK 292


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: 260
Number of extensions: 20
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: 293
Length adjustment: 26
Effective length of query: 270
Effective length of database: 267
Effective search space:    72090
Effective search space used:    72090
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