GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Porphyrobacter dokdonensis DSW-74

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_068865576.1 I603_RS12545 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_001677335.1:WP_068865576.1
          Length = 445

 Score =  158 bits (399), Expect = 4e-43
 Identities = 150/463 (32%), Positives = 234/463 (50%), Gaps = 45/463 (9%)

Query: 2   RLFGTAGIRGTLWEKV-TPELAMKVGMAVGTY--KSG---KALVGRDGRTSSVMLKNAMI 55
           +LFGT GIRG   + V T   AMKVG A G +  + G   + ++G+D R S  M+++A++
Sbjct: 4   KLFGTDGIRGRTNDGVMTAATAMKVGQAAGRHFVRGGHRHRVVIGKDTRLSGYMMESALV 63

Query: 56  SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114
           +G  S G++V+    +PTPA+A  TR++ AD GVMI+ASHN   DNG+K+F  DG +   
Sbjct: 64  AGFTSVGIDVIMTGPLPTPAIALLTREMRADLGVMISASHNLFADNGIKLFGPDGFKLSD 123

Query: 115 EQERGLEEIIFSGNFRKARWDEIKPVRNVEVIPD-YINAVLDFVGHETN---LKVLYDGA 170
             E  +E ++ +     A  + I   R +E     YI+AV   V  E     LKV+ D A
Sbjct: 124 AAEAEIERLMET-EIPLAPPERIGRARRIEDARGRYIHAVKQSVATEIRFDGLKVVVDCA 182

Query: 171 NGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQ 230
           NGA   VAP  + E+GA V+++    +G             IA L   V E G D+ IA 
Sbjct: 183 NGAAYQVAPSAIWELGADVVTLGVTPNG--TNINDGVGSTAIAALQAKVVEEGADIGIAL 240

Query: 231 DGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRIDAVVERAG 287
           DGDADR+ V DEKG  VD D ++AL A   ++E G   GG +V ++ +   ++  +   G
Sbjct: 241 DGDADRLIVVDEKGRAVDGDQIMALIA-TRMQERGSLRGGGIVATVMSNLGLERYLAGLG 299

Query: 288 GRVVRIPLGQPHDGIKRYKA----IFAAEPWKLVHPKFGPWIDPFV-TMGLLIKLIDENG 342
             +VR  +G  +  ++  KA    +   +   ++   +    D  V  + +L  L+    
Sbjct: 300 LDLVRTKVGDRY-VLEAMKAGGYNVGGEQSGHMILLDYATTGDGTVAALRVLASLVRSGK 358

Query: 343 PLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSE-IKEVLTISGFRIALN 401
             SEL+           +V  P     ++++    E  + L +E +K V+  +   +A  
Sbjct: 359 KASELL-----------HVFDP---VPQLLKNVRYEGGQPLENEGVKTVIAAAEAELA-- 402

Query: 402 DGSWILIRPSGTEPKIRVVAE----APTEKRRDELFEMAYSTV 440
               ++IRPSGTEP IRV+AE    A  E+  D + E  ++ V
Sbjct: 403 GKGRLVIRPSGTEPVIRVMAEGDDQAQVERVVDTICEAVHAAV 445


Lambda     K      H
   0.318    0.138    0.402 

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: 492
Number of extensions: 36
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 450
Length of database: 445
Length adjustment: 33
Effective length of query: 417
Effective length of database: 412
Effective search space:   171804
Effective search space used:   171804
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: 51 (24.3 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