GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1896 in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate 3608246 Dshi_1650 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>lcl|FitnessBrowser__Dino:3608246 Dshi_1650
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 385

 Score =  114 bits (286), Expect = 3e-30
 Identities = 65/208 (31%), Positives = 101/208 (48%), Gaps = 1/208 (0%)

Query: 74  FWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133
           F+N++ +T+PA +I   + A   Y L+   F G  L   L++    +P Q  L+P     
Sbjct: 178 FFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLH 237

Query: 134 GKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKILLP 193
              G+     G  L H  +G+       RNY V +P  +++ A++DGA  F IF KI+LP
Sbjct: 238 NAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLP 297

Query: 194 MSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVN-TSTGAKEYNVDMAAA 252
           +S P +    I+QF   WND L   VF        TV  N +V    T    + +   AA
Sbjct: 298 LSFPALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAA 357

Query: 253 MIAGLPTLLVYIFAGKYFLRGLTSGAVK 280
            ++    LLV+    ++ +RGL +G+VK
Sbjct: 358 FVSIAVPLLVFFSMQRFLVRGLLAGSVK 385


Lambda     K      H
   0.329    0.143    0.447 

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: 290
Number of extensions: 20
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: 281
Length of database: 385
Length adjustment: 28
Effective length of query: 253
Effective length of database: 357
Effective search space:    90321
Effective search space used:    90321
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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