GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Kocuria flava HO-9041

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_058859757.1 AS188_RS05785 carbohydrate kinase

Query= reanno::pseudo3_N2E3:AO353_25910
         (314 letters)



>NCBI__GCF_001482365.1:WP_058859757.1
          Length = 309

 Score =  173 bits (438), Expect = 5e-48
 Identities = 116/316 (36%), Positives = 159/316 (50%), Gaps = 15/316 (4%)

Query: 1   MYLVCGEALFDFFSENAASSQASTVNYKAIAGGSPFNVAVGLRRLGVDSALFAGLSTDYL 60
           M  V GEAL D  S+     +A        AGGSP NVAVGL RLG +         D  
Sbjct: 1   MLTVIGEALVDVVSKQGQEPRAH-------AGGSPMNVAVGLARLGHEVQFLGRYGGDEH 53

Query: 61  GRRLQQVLADEGVRADYLLDFDAPTTLAMVAVGANGSPHYSFRGEGCADRQLTLAHLPEL 120
           G R+Q  L D GVR  +  D   PT++A   +  +G+  Y FR +   +  L    L  L
Sbjct: 54  GTRVQAHLRDNGVRLPFEPD-TRPTSVAEAVIDDDGAATYDFRLDWSLE--LDDDRLERL 110

Query: 121 SDEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIELWRSRIAEL 180
                 LH+GS   +++P A  +   V    G+ ++S DPN R +  PD    R+R  EL
Sbjct: 111 LAGTELLHVGSIGAMLEPGASRVRRAVELAHGRAVVSYDPNCRPSIIPDSSAARARAEEL 170

Query: 181 MKYADLIKVSDEDLSLLYPGREPQSVIDSWLEHRCQLVFLTRGGQGATVFSRRHG--SWS 238
           +  AD++K SDEDL  LYP R  +    +WL    +LV +TRG  G    +R  G     
Sbjct: 171 VALADVVKASDEDLLWLYPHRSVEETAAAWLRAGARLVVVTRGPMGPWARTRATGPRGVE 230

Query: 239 APASKVVIADTVGAGDTFQAALITWLTEQQLDSVDGLQR---LSREQIDAMLRFAISAAA 295
            PA++  + DTVGAGD+F AA + WL +         +R   L   Q++ +LRFA +AAA
Sbjct: 231 VPAARAEVVDTVGAGDSFMAATLGWLADHGYTGATARERIDDLDAGQVEDLLRFAAAAAA 290

Query: 296 LTCSKTGPDLPYRHQL 311
           +T S+ G DLP R  L
Sbjct: 291 VTVSRAGADLPRREDL 306


Lambda     K      H
   0.320    0.136    0.398 

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: 255
Number of extensions: 15
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: 314
Length of database: 309
Length adjustment: 27
Effective length of query: 287
Effective length of database: 282
Effective search space:    80934
Effective search space used:    80934
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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