GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cola:Echvi_1022
          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:

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