GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Nocardioides daejeonensis MJ31

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_110207115.1 DNK54_RS11370 ribokinase

Query= reanno::pseudo5_N2C3_1:AO356_00950
         (304 letters)



>NCBI__GCF_003194585.1:WP_110207115.1
          Length = 310

 Score =  187 bits (476), Expect = 2e-52
 Identities = 132/309 (42%), Positives = 172/309 (55%), Gaps = 12/309 (3%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60
           M  +VVV+G+LN+DLV + PRLP  GET++G       GGKGAN AVAAAR GA+V  VG
Sbjct: 1   MTPRVVVVGALNVDLVVKVPRLPGPGETVVGPEVQRHGGGKGANAAVAAARAGAEVRYVG 60

Query: 61  CVGDDAYGEQLRGALLAEGIDCQAVRVEQG-SSGVALIVVDDNSQNAIVIVAGANGALTA 119
            VG D  G      L+AE ID   V VE G ++G ALIVVD   +N I + AGAN  ++ 
Sbjct: 61  AVGADDLGTGALAELVAENIDVSGVVVEPGVATGTALIVVDHAGENQIAVAAGANAVVSP 120

Query: 120 EVLDGVDDVLQS----ADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADW 175
           E    V  VL      A  ++   E+P   V  A++  RA     +LNPAP +  L A  
Sbjct: 121 E---SVRQVLARSRGWATCVLVSTEIPMDAVVAAVETARAYDLPCVLNPAPVAAGL-AGL 176

Query: 176 YACIDYLIPNESEAAVLSGLAVDSLETA-EAAAAHLIAAGAGKVIVTLGAQGLMFAN-GA 233
            +    L PN+ E   L     +  ET+ EA A+ +  +    V VTLGA G+M A+   
Sbjct: 177 VSMSPVLTPNQGELRDLCRALGEPDETSLEAMASAVAHSSKAAVAVTLGADGVMVADPDG 236

Query: 234 SFEHFP-APRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPS 292
           S  H P AP  + VDTT AGDTF G  AAALA G++   A+R G  AA++SV  AGA+  
Sbjct: 237 STCHIPAAPVAEVVDTTGAGDTFNGVLAAALASGETISGAVRRGVAAASISVGSAGARAG 296

Query: 293 IPTLLEVQA 301
           +PT   + A
Sbjct: 297 MPTAEVIDA 305


Lambda     K      H
   0.318    0.133    0.377 

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: 316
Number of extensions: 16
Number of successful extensions: 5
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: 304
Length of database: 310
Length adjustment: 27
Effective length of query: 277
Effective length of database: 283
Effective search space:    78391
Effective search space used:    78391
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 (21.7 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