GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Caldicellulosiruptor kronotskyensis 2002

Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate WP_013429643.1 CALKRO_RS03030 alpha-xylosidase

Query= CAZy::AAO75446.1
         (748 letters)



>NCBI__GCF_000166775.1:WP_013429643.1
          Length = 772

 Score =  384 bits (987), Expect = e-111
 Identities = 211/577 (36%), Positives = 315/577 (54%), Gaps = 30/577 (5%)

Query: 174 RYDGLPIAFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNN 233
           +Y G  I     T  +E+ +LS      EC  G GERF     +GQ + + N+DG G N+
Sbjct: 135 KYLGYAIMPDNTTYMREQLSLSV----GECVYGLGERFTPFVKNGQVIDMWNEDG-GTNS 189

Query: 234 RRTYKNIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEI 293
              YKNIPFY+++R YG F +        +A  +   VQF  +   L+ F+I G  M+ +
Sbjct: 190 DLAYKNIPFYITNRGYGVFVNDPGRVSFEVATENVERVQFSVEGEYLEYFIIGGSNMKNV 249

Query: 294 LRGYRDLTGYPSMPPLWSFGVWMSRMTYFSADE--VNEICDRMRAEHYPCDVIHLDTGWF 351
           L  Y  LTG P +PP WSFG+W++     S DE  V    D M  +  P  V H D  W 
Sbjct: 250 LENYTKLTGRPQLPPAWSFGLWLTTSFTTSYDEKTVTNFIDGMIEKDIPLHVFHFDCFWM 309

Query: 352 RTDWLCEWKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLT 411
           +     +++++   FP+P   ++RLK+ G ++ +W  PYV++ ++  +E K   Y     
Sbjct: 310 KDMHWVDFEWDRRVFPEPSQMLKRLKEKGVKICVWINPYVSQFSKLFDEGKEKGYFL--- 366

Query: 412 KQQDTDGSNFSALDYA---GTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDA 468
             +  +G  +   D+      +DFT P+A  WY   LK+L+ MGV C KTDFGE I  D 
Sbjct: 367 --KKPNGDVWQTDDWQPGMAIVDFTNPEACRWYSEKLKELIKMGVDCFKTDFGERIPTDV 424

Query: 469 VY-KGMKPELLNNLYALLYQKAAYEITKEVTGDG--IVWARAAWAGCQRYPLHWGGDSCS 525
           VY  G  P+ ++N Y  LY K  YE  +E  G G  +V+AR+A AG Q++P+HWGGD  +
Sbjct: 425 VYFDGSDPQKMHNYYTYLYNKTVYETLQETFGKGNAVVFARSATAGSQKFPVHWGGDCLA 484

Query: 526 SWDGMAGSLKGGLHFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIR 585
           S++ MA +L+GGL   L GF FWSHD+ GF        S    D+Y RW  FG+ +SH R
Sbjct: 485 SYESMAETLRGGLSLSLCGFGFWSHDIGGFE-------STATPDLYKRWVAFGLLSSHSR 537

Query: 586 YHGTNK-REPWHYPAIAPLVKKWW-KLRYSLIPYIIEQSKLAVESGWPLLQALILHHPED 643
            HG +  + PW Y   A  V +++ KL+  L+PYI   +  A E G P+L+ ++L  P+D
Sbjct: 538 LHGNSAYKVPWLYDEEAVDVLRFFTKLKCKLMPYIFSAAVEATERGIPVLRPMVLEFPDD 597

Query: 644 KLCWHIDDEYYFGNDFLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLE 703
             C ++D +Y  G+  LVAP+ + +   + Y+PEG W N  TGE+++GG+W KE +    
Sbjct: 598 PACVYLDRQYMLGDSLLVAPIFSEDGYVEYYVPEGIWTNILTGEKVEGGKWRKEKH-GYF 656

Query: 704 EMPVYVRENAVIPIYPEEVNCTDEMDLGKSIALRIDH 740
            +P+  R N VIPI     +   + D   ++A+ I H
Sbjct: 657 SLPLLARPNTVIPI--GSCDTRPDYDYADNVAMNIYH 691


Lambda     K      H
   0.322    0.139    0.449 

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: 1671
Number of extensions: 64
Number of successful extensions: 8
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: 748
Length of database: 772
Length adjustment: 40
Effective length of query: 708
Effective length of database: 732
Effective search space:   518256
Effective search space used:   518256
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 (21.9 bits)
S2: 55 (25.8 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