GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Herbaspirillum seropedicae SmR1

Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate HSERO_RS02995 HSERO_RS02995 ABC transporter permease

Query= BRENDA::P68183
         (296 letters)



>FitnessBrowser__HerbieS:HSERO_RS02995
          Length = 291

 Score = 57.8 bits (138), Expect = 3e-13
 Identities = 64/210 (30%), Positives = 92/210 (43%), Gaps = 28/210 (13%)

Query: 100 VALSTTCAYAFARMRFPGKATLLKGMLIFQM-FPAVLSLVALYALFDRLGEYIPFIGLNT 158
           +A+S        R RFPG+A LL  ML F + FP V+    +  L  R G     IG  T
Sbjct: 91  LAISVFVGLFLQRHRFPGQALLL-AMLTFPLAFPGVVVGFMVIMLAGRQG----LIGALT 145

Query: 159 HG----GVIFAY-LGGIALH---------VWTIKGYFETIDSSLEEAAALDGATPWQAFR 204
           +G     ++FAY L G+ L          + T+    E +D SLEEAA   GA PWQ   
Sbjct: 146 NGLFGESLVFAYSLAGLFLGYLYFSIPRVILTVVAAAEKLDPSLEEAARSLGARPWQVLL 205

Query: 205 LVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWGDFA 264
            V+LP  +P L     + F  ++     A  L  +++   + +    Y     Y   +FA
Sbjct: 206 HVVLPALLPALVSSGAICFATSVGAFGTAFTLAANIDVLPMTI----YNEFTGY--ANFA 259

Query: 265 AAAVMSALPITIVFLLAQRWLVNGLTAGGV 294
            AA +S +   I + +    L   LT  GV
Sbjct: 260 TAASLSIVLGVITWAVLA--LARSLTGSGV 287


Lambda     K      H
   0.328    0.141    0.435 

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: 224
Number of extensions: 14
Number of successful extensions: 2
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: 291
Length adjustment: 26
Effective length of query: 270
Effective length of database: 265
Effective search space:    71550
Effective search space used:    71550
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 (21.8 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