GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Magnetospirillum magneticum AMB-1

Align CAC0385 (EC 3.2.1.86) (characterized)
to candidate WP_011382666.1 AMB_RS01115 beta-glucosidase

Query= CAZy::AAK78365.1
         (469 letters)



>NCBI__GCF_000009985.1:WP_011382666.1
          Length = 453

 Score =  293 bits (749), Expect = 1e-83
 Identities = 166/468 (35%), Positives = 249/468 (53%), Gaps = 43/468 (9%)

Query: 2   KFPKDFFLGAASASYQVEGAWNEDGKGVSNWDVFTKIPGKTFEGTNGDVAVDHYHRYKED 61
           +FPKDFF GA++A+YQ+EGA++ DG+G++ WD FT   GK  +G++  VA DHYHRY ED
Sbjct: 16  QFPKDFFWGASTAAYQIEGAYDTDGRGMTIWDKFTA-DGKIMDGSSAKVACDHYHRYPED 74

Query: 62  VKLMAEMGLDSYRFSVSWPRIIPDGDGEINQKGIEFYNNLIDECLKYGIVPFVTLYHWDM 121
           + LM   G ++YRFS++WPRIIP G G IN KG++FY+ L+D+ L+ GI P   LYHWD+
Sbjct: 75  IALMKAAGFNAYRFSLAWPRIIPAGTGAINAKGLDFYDRLVDKILEAGIKPMACLYHWDL 134

Query: 122 PEVLEKAGGWTNKKTVDAFVKYAKACFEAFGDRVKRWITFNETIVFCSNGYLSGAHPPGI 181
           P+ LE  GGW  +  V  F +YA+   +  GDRVK W   NE  V    GY  G H PG 
Sbjct: 135 PQPLEDKGGWQGRDIVGPFAEYARIATKRLGDRVKDWYMLNEPNVVAIIGYGIGEHAPGY 194

Query: 182 TGDVKKYFQATHNVFTAHARSVIEYKKLKQYGEIGITHVFSPAFSVDDKEENKAAAYHAN 241
                   +A H+   A   ++   +       +G      P  S DD  +N+AAA    
Sbjct: 195 KLGEDGILKALHHQNLAQGTALRAIRAEHSDAVLGTVINLQPCRSQDDDPKNRAAAI--- 251

Query: 242 QYEITWY---YDPILKGKYPEYV---IKNIEKQGFLPDWTDEELNTLREAAPLNDFIGLN 295
           +++  W     D +++G  P+ +   + +I K G        ++ T++   P+ D +G+N
Sbjct: 252 RWDAVWNRVPLDGVMRGAIPDVLAEKMAHIVKPG--------DMETIK--FPI-DMLGIN 300

Query: 296 YYQPQRVIKNHDTGEKIERTRENSTGAPGNASFDGFYRTVKMDDKTYTKWGWEISPESLI 355
           YY   R+   H+ G                  FD F+     D   +T   W + P+ L 
Sbjct: 301 YY--SRMTMKHEEGH----------------PFDVFWGDAHCD--RWTAMAWPVQPDGLY 340

Query: 356 LGLEKLKEQYGDIKIYITENGLGDQDPIIED-EILDMPRIKFIEAHLRAIKEAISRGINL 414
             L + KE YG+  ++I ENG    D +  D ++ D  R+ FI  H+  +  A+  G N+
Sbjct: 341 DLLREFKELYGNPAVFIAENGAAYDDVVTPDGQVHDAERVAFIRDHVSEVARAVKDGCNV 400

Query: 415 KGYYAWSVIDLLSWLNGYKKQYGFIYVDHKHNLDRKKKLSFYWYKKVI 462
           KGY  WS++D   W  G  K++G + VD++  L R  K S+ W+ +VI
Sbjct: 401 KGYLVWSLLDNFEWAYGLSKRFGIVRVDYE-TLKRTPKDSYKWFAEVI 447


Lambda     K      H
   0.318    0.138    0.433 

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: 651
Number of extensions: 28
Number of successful extensions: 4
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: 469
Length of database: 453
Length adjustment: 33
Effective length of query: 436
Effective length of database: 420
Effective search space:   183120
Effective search space used:   183120
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: 51 (24.3 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