GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Caldicellulosiruptor kronotskyensis 2002

Align α-glucosidase / binding-toxin receptor (Agm3;AgAgm3) (EC 3.2.1.20) (characterized)
to candidate WP_013429333.1 CALKRO_RS01320 alpha-amylase

Query= CAZy::ABW98683.1
         (588 letters)



>NCBI__GCF_000166775.1:WP_013429333.1
          Length = 514

 Score =  215 bits (547), Expect = 4e-60
 Identities = 157/497 (31%), Positives = 244/497 (49%), Gaps = 61/497 (12%)

Query: 41  FYQIYPRSFQDSNGDGIGDLKGITARMEYLAGLGIDATWLSPPFVSPLADFGYDVADFYD 100
           FY+++ RSF DSNGDGIGD+ G+  ++ Y+  LG++A WL P F SP +  GYDV ++Y 
Sbjct: 42  FYEVFVRSFYDSNGDGIGDINGLAEKLPYIKSLGVNAIWLMPIFESP-SYHGYDVTNYYK 100

Query: 101 IQPEYGTLADMEELIAEAHRHGIKLMLDFIPNHSSDEHDWFVQ-SANGVAKYRDYYIWRP 159
           + P+YGT  D    I +AH+ GIK+++D + NH+S +H WF++ S+N  +KYR+YYIW  
Sbjct: 101 VNPDYGTNEDFVNFIKKAHKMGIKVIIDMMINHTSSKHPWFIEASSNKNSKYRNYYIWAT 160

Query: 160 GRQNSQTGALEPPNNWISVFGGPAWTYDERRGEFYLHQ-FTKKQADLNYRNPAVVEEMTK 218
              N     L+ P    S  G   W    ++G+ Y +  F  +  DLN+ N AV EEM K
Sbjct: 161 PNTN-----LDEP----SELGTRQW---YKKGDSYYNAIFWSEMPDLNFDNKAVREEMKK 208

Query: 219 MLSFWLEKGVDGFRLDAINHMFEDAQLRDEPPGWGAPGTYDELDHIYTKDNPDTYNVVYG 278
           +  FWLEKGVDGFRLDA  H++  ++ +D    W      +E          D Y V   
Sbjct: 209 IAKFWLEKGVDGFRLDAAKHIYPLSREKDTLVWW------EEYAKFCRSIKKDVYLVAEV 262

Query: 279 WRQLCDDFGRRMNKTIIIMTEAYASIENTMLYYEDATGTRQGAHMPFNFQLIYDFRHD-Q 337
           W  L     +R+ +        YA I ++   +  A    +G        +IY+     Q
Sbjct: 263 WDSL-----QRIAQ--------YAKIFDSCFNFIIAQNIIEG--------VIYENTQTLQ 301

Query: 338 NAIGLKQSIDFWLNHMPARHTASWVAGSHDHSRVGSRVGL-EHVDQVLTLLHTLPGTSIT 396
           N   L    + + N  P    A ++  +HD +R  + +G    +     LL TLPG    
Sbjct: 302 N--NLSSIYNLYKNVNPQFVDAPFLT-NHDMNRAYTEIGSNSKMKLAAALLLTLPGNPFI 358

Query: 397 YYGEEIGMLDFKDAQLYDNRDPNRTPMQWDNSISAGFSTNRTTWLRLHPDYPTRNVAMQE 456
           YYGEEIGM   K  +        R P +W  +   G +    +     PD    +V  QE
Sbjct: 359 YYGEEIGMKGQKPDEYI------REPFKWYETWKKGQTNWEMSLYNSGPD--VASVEKQE 410

Query: 457 AAEKSTLKHFRTLTALR-RHPTLVHGEFKHRTVGPDVYAFSRELHGEDTLVTVLNMATSS 515
             + S L  +R + + R ++  L+ G+F+      D+ +F+R ++    +V + N     
Sbjct: 411 KDKNSLLNFYRDMISFRKKNLPLLKGDFQLIKTSFDILSFAR-VYNNQKMVVIFNFTGK- 468

Query: 516 RTVDLGDFVNLPARLTV 532
              +L   +NLP+ + +
Sbjct: 469 ---ELSKTINLPSNINI 482


Lambda     K      H
   0.320    0.136    0.423 

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: 788
Number of extensions: 46
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: 588
Length of database: 514
Length adjustment: 36
Effective length of query: 552
Effective length of database: 478
Effective search space:   263856
Effective search space used:   263856
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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