GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Sphingobium czechense LL01

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate WP_066608734.1 V473_RS17575 DUF3459 domain-containing protein

Query= uniprot:H3K096
         (538 letters)



>NCBI__GCF_001046645.1:WP_066608734.1
          Length = 535

 Score =  549 bits (1415), Expect = e-161
 Identities = 271/533 (50%), Positives = 349/533 (65%), Gaps = 13/533 (2%)

Query: 7   WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66
           WW+G VIYQIYPRSF DS  DG+GDLNGIT++L+++A L  D IW+SPFFTSPM DFGYD
Sbjct: 12  WWKGAVIYQIYPRSFQDSNHDGIGDLNGITQRLEHIARLGADAIWISPFFTSPMRDFGYD 71

Query: 67  VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126
           ++DY DVDP+FGTL DF AL+ +AH+LGLKV IDQV +HTSD H WF +SR +RT+ KAD
Sbjct: 72  IADYCDVDPIFGTLADFDALVARAHALGLKVTIDQVYAHTSDLHDWFAQSRASRTSEKAD 131

Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186
           WFVW DPK DGTPPNNW S+FGG AWT+D+RR QYY+H FL+SQP +N H+P  + A LD
Sbjct: 132 WFVWVDPKEDGTPPNNWQSVFGGPAWTWDARRGQYYMHQFLSSQPQLNLHNPAVQDALLD 191

Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246
            MRFWLD GVDGFRLD +N   HD +LRDNPP P       G P    + +Q   Y  S 
Sbjct: 192 AMRFWLDRGVDGFRLDALNHSMHDPQLRDNPPAP-----DTGKPRTRSFDFQIKTYSQSH 246

Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH-S 305
           P  +DF+K +R L DEY    TV E+G D     M  YTAG   L+ AY F+ L     +
Sbjct: 247 PGVVDFIKRIRTLCDEYGAIFTVAEVGGDLSETEMKAYTAGETHLNSAYGFNFLYADALT 306

Query: 306 ASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLRGSV 365
            + + + ++R+    G  WP WA  NHD  R+ +RW A ED  A+ ++   +L +LRG+ 
Sbjct: 307 PALVADTVDRWPDEPGMGWPSWAFENHDAPRALSRWCAAEDRPAFGRLKAMLLVALRGNA 366

Query: 366 CLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPW-TDGEQGGFSPVEPWL 424
            LYQGEELG+ + D+PF+++QDP     WP    RDG RTP+PW  D  Q GFS VEPWL
Sbjct: 367 ILYQGEELGITQVDIPFDKLQDPEAIANWPLTLSRDGARTPLPWAADAAQAGFSSVEPWL 426

Query: 425 PMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQKG 484
           P  A HL LAV  Q+ DP + LN  RA+LA R+++PAL  G L ++   D  L F R   
Sbjct: 427 PHGADHLALAVDAQEADPASLLNHTRAMLALRKANPALRHGSLEILVADDQRLLFRRAAD 486

Query: 485 DETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTATRDGSTL-TLPAYQAAFMQ 536
            ++LLC+FNL+   +  T P E+A   P     +  +G+T   LP + A  ++
Sbjct: 487 GQSLLCLFNLSA--KPATWPEEIA---PTNKLLSAVNGATPGALPPFGALMIE 534


Lambda     K      H
   0.320    0.138    0.443 

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: 943
Number of extensions: 43
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: 538
Length of database: 535
Length adjustment: 35
Effective length of query: 503
Effective length of database: 500
Effective search space:   251500
Effective search space used:   251500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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