GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglK in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= reanno::Smeli:SMc03065
         (362 letters)



>lcl|FitnessBrowser__Cola:Echvi_1022 Echvi_1022 ABC-type
           spermidine/putrescine transport systems, ATPase
           components
          Length = 345

 Score =  149 bits (377), Expect = 8e-41
 Identities = 106/340 (31%), Positives = 171/340 (50%), Gaps = 27/340 (7%)

Query: 19  IHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERV----NDVPPSK 74
           +  I ++I+EG     VG +G GK+TLL++IAGLE    G++   G+ +    + +P ++
Sbjct: 21  VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQTIVNGKSALPANQ 80

Query: 75  RGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAA-DMLQLTPYLDRL--- 130
           R + ++FQ YAL+P MT+ +N+       RE+  +  R  R  A D L L    D     
Sbjct: 81  REVGVIFQEYALFPQMTLLENV-------REALHQESRNARQIAMDSLALAGLEDSFSAY 133

Query: 131 PKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIY 190
           P  LS GQRQR A+ RA+   PK+ L D+P  +LD   +     +I  +  + +  T I 
Sbjct: 134 PHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIV-KATGITAIV 192

Query: 191 VTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITAT 250
            +H   +A++LAD I +L  G ++QVG P+E+Y++PAN +VA F G    N + AT T  
Sbjct: 193 ASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGK--RNELLATPTED 250

Query: 251 GQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEGTVSIVEALGE 310
           G              +  P +AS   K      R ED ++ ++ +    G V+ V   G+
Sbjct: 251 GFYAGFGF-------IPHPDSASYTDKVKIL-FRSEDAKIKKSTEQPLSGIVTRVLFYGD 302

Query: 311 VTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKL 350
             ++ +E     +  I   PG      G ++ FT DK ++
Sbjct: 303 HQIVKLEDDEGKQISIKAAPG-RNFEMGARMFFTIDKFEI 341


Lambda     K      H
   0.320    0.137    0.387 

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: 266
Number of extensions: 14
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: 362
Length of database: 345
Length adjustment: 29
Effective length of query: 333
Effective length of database: 316
Effective search space:   105228
Effective search space used:   105228
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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 preprint 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