GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Methanospirillum lacunae Ki8-1

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_109968442.1 DK846_RS08105 phosphopentomutase/phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_003173355.1:WP_109968442.1
          Length = 418

 Score =  201 bits (512), Expect = 3e-56
 Identities = 147/452 (32%), Positives = 224/452 (49%), Gaps = 47/452 (10%)

Query: 3   LFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKALVGRDGRTSSVMLKNAMISGLLSTG 62
           LFG++GIR  L+++    LAM+VGMAVG  ++ + LVG D RT+   L ++ I+G+  TG
Sbjct: 2   LFGSSGIR-RLYDQDLLSLAMQVGMAVGN-RADQVLVGMDSRTTGPALSSSFIAGICYTG 59

Query: 63  MEVLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEE 122
            + L   + PTP++A+  R    A  M+TASHNP   NG+K+FN DG+ F   Q+  +E+
Sbjct: 60  AKALQGGIAPTPSIAYCCRSFK-AACMVTASHNPEPYNGLKLFNPDGSSFQALQQDEIED 118

Query: 123 IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLL 182
            I     R A W         + +  + +A+L  +  + +L V+ D  NGAGS++ P+LL
Sbjct: 119 AISDN--RTADWLSQGETMKYDPLTPHHDAILSEIDVKKDLPVILDCGNGAGSVLTPHLL 176

Query: 183 REMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242
            + GA V++VNA+  G F  R  EP  EN+ YL  L++++    A+  DGDADR+  FD 
Sbjct: 177 SDAGASVVAVNANPSGIF-SRPSEPLVENLPYLPALMKKVNARCAVVHDGDADRMMAFDN 235

Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302
            G Y+  D ++ LFAK      G   VV + D    ++ + E     V R P+G      
Sbjct: 236 TGTYIPGDLLLILFAKYL----GAKRVVTTYDASMAVEEIAE-----VRRTPVGDAFVSE 286

Query: 303 KRYK-AIFAAEPWKLVHPKFGPWIDPFVT--------MGLLIKLIDENGPLSELVKEIPT 353
           +  +   F  EP        G WI P ++         GL  ++  E   ++E +  IP 
Sbjct: 287 QLVQWGDFGGEP-------SGAWIFPQISYCPDGPFAAGLFCEMAGE-WNIAEELASIPK 338

Query: 354 YYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILIRPSGT 413
           Y + + +   P  ++      AA   +              G R+  +DG W L+R SGT
Sbjct: 339 YPILRRSQQFPQSHEILYALGAANPTD--------------GLRLEEDDG-WCLVRASGT 383

Query: 414 EPKIRVVAEAPTEKRRDELFEMAYSTVSRIVK 445
           EPKIR  AE  T      + E     V   +K
Sbjct: 384 EPKIRFTAEGRTLDDAKRMLERGEEMVRLALK 415


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: 461
Number of extensions: 26
Number of successful extensions: 6
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: 450
Length of database: 418
Length adjustment: 32
Effective length of query: 418
Effective length of database: 386
Effective search space:   161348
Effective search space used:   161348
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