GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Sphingomonas koreensis DSMZ 15582

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::P54933
         (332 letters)



>FitnessBrowser__Korea:Ga0059261_1321
          Length = 238

 Score =  115 bits (289), Expect = 8e-31
 Identities = 78/223 (34%), Positives = 117/223 (52%), Gaps = 15/223 (6%)

Query: 4   ITLRNVQKRFGEAVV----IPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQ 59
           I LRN+ K FGE       +  +DLDI + +FV  +GPSG GKST + ++  L+  + G+
Sbjct: 8   IRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTSGE 67

Query: 60  IMIDG-------RDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIER 112
            +  G       RD   +   K  L  VFQ + L       +N+  PL + + E +++  
Sbjct: 68  FLFKGVYIETLDRDQRALVRRKY-LGFVFQGFNLLSRTNALENVELPL-LYRGEDKKVRH 125

Query: 113 RVSNAA-KILNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVN 171
            +  AA + + L ++ D  P +LSGGQ QRVAI RAIV  PA  L DEP  NLD+A  V 
Sbjct: 126 ELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSVE 185

Query: 172 MRLEITELHQSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQ 214
           +   +T L++    T++ VTH+  +    A  IV    G +E+
Sbjct: 186 IMELLTSLNKDSGITVLMVTHEP-DMAAFARTIVHFKDGLVER 227


Lambda     K      H
   0.320    0.137    0.400 

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: 169
Number of extensions: 8
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: 332
Length of database: 238
Length adjustment: 26
Effective length of query: 306
Effective length of database: 212
Effective search space:    64872
Effective search space used:    64872
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: 47 (22.7 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