GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Klebsiella michiganensis M5al

Align ribokinase (EC 2.7.1.15) (characterized)
to candidate BWI76_RS23680 BWI76_RS23680 ribokinase

Query= BRENDA::A0A0H2UL04
         (309 letters)



>FitnessBrowser__Koxy:BWI76_RS23680
          Length = 313

 Score =  199 bits (505), Expect = 9e-56
 Identities = 127/296 (42%), Positives = 168/296 (56%), Gaps = 2/296 (0%)

Query: 6   KLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVG 65
           K+ V GS N D V +V  FP PGE+L         GGKGANQA AA +  A+V +I  +G
Sbjct: 4   KVCVFGSFNFDMVARVERFPVPGESLVACGSMTSAGGKGANQATAALKAGANVHYIGKIG 63

Query: 66  DDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVS-DSGENSICISAEANAKLTAAA 124
           +D+FG   R   K  G N   + +  + PTG A+I V+ +  EN I +   AN  ++   
Sbjct: 64  NDTFGHFARRHLKGVGFNAVTLLVAEDIPTGNALIYVAGNDAENMIAVDPGANMTVSDDE 123

Query: 125 IEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLI 184
           I   + AI  A  +L+QLE  L  I +    AK A   V+LNPAP + + +  L  VDL+
Sbjct: 124 IAGCVPAIGCADVVLVQLENNLSAIERVVDAAKAAGAFVVLNPAPWQPVDNAFLSKVDLL 183

Query: 185 TPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFV 244
           TPN TEA ++TG  V   ++A +AADALH +G   VIITLG+KG  LS+ G    IP F 
Sbjct: 184 TPNATEAGLMTGCQVDSLAAAAEAADALHAQGARNVIITLGAKGALLSEQGVKSPIPCFP 243

Query: 245 VKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAE 300
               DTT AGD FNGAL   L    PL +A +FA A AA+SV + GA +S+P   E
Sbjct: 244 SHPRDTTGAGDAFNGALAARLACGEPLHTAARFAAAYAAVSVEKQGA-SSLPDYEE 298


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: 220
Number of extensions: 12
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: 309
Length of database: 313
Length adjustment: 27
Effective length of query: 282
Effective length of database: 286
Effective search space:    80652
Effective search space used:    80652
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