GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Klebsiella michiganensis M5al

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS14585 BWI76_RS14585 ribokinase

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS14585
          Length = 290

 Score =  126 bits (316), Expect = 7e-34
 Identities = 93/306 (30%), Positives = 138/306 (45%), Gaps = 29/306 (9%)

Query: 6   KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVG 65
           ++ V G++  D    +P  P+ G ++HG       GGKGANQA+  AR   +   IA  G
Sbjct: 2   RVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILARCGIETRLIAATG 61

Query: 66  DDSFGINIRESFKLDGINTAGVKLQP----NCPTGIAMIQVSDSGENSICISAEANAKLT 121
           +DS G+ IR+  K + +      L P    N  +  ++I  S  G+N+I  +  A     
Sbjct: 62  NDSNGVWIRQQIKNEPLT-----LLPDGHFNQHSDTSIILNSADGDNAIITTTAAADTFR 116

Query: 122 AAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCV 181
              I P +A       LL Q    LD      Q AK+     + NP+P       L   +
Sbjct: 117 LDDIIPHIADAVAGDILLQQGNFSLDKTRALFQYAKSRSMTTVFNPSPVNPEFCHLWPLI 176

Query: 182 DLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIP 241
           D+   NE+EAE+L                     G++ ++IT G+ G WL Q G+ +  P
Sbjct: 177 DIAVVNESEAELLQPY------------------GVKSLVITQGAAGAWLVQEGQRRFCP 218

Query: 242 GFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHA--AAAISVTRFGAQTSIPTRA 299
               +A DTT AGDTF   ++   L       A+  AHA  AAAI+V+R G  ++ P   
Sbjct: 219 AVPAEALDTTGAGDTFLAVMLASALLRDVAPDALALAHASRAAAITVSRRGTLSAFPGSH 278

Query: 300 EVEAFL 305
           E+ A L
Sbjct: 279 ELAALL 284


Lambda     K      H
   0.316    0.132    0.373 

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: 173
Number of extensions: 10
Number of successful extensions: 3
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: 309
Length of database: 290
Length adjustment: 27
Effective length of query: 282
Effective length of database: 263
Effective search space:    74166
Effective search space used:    74166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 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