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_013429617.1 CALKRO_RS02895 alpha-xylosidase

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



>NCBI__GCF_000166775.1:WP_013429617.1
          Length = 759

 Score =  764 bits (1972), Expect = 0.0
 Identities = 349/749 (46%), Positives = 510/749 (68%), Gaps = 5/749 (0%)

Query: 1   MKPTNYHLFDFLDFDTELLRDESLWKACKPTAVYEK-DGDICVTVPFQKQLLANDMVADT 59
           MK  N   +D LDFD    +++ LW A     VYE+ DG + + +PFQ Q      V D 
Sbjct: 1   MKQKNSFKYDMLDFDLPEAKNDILWIAEMAEEVYEQSDGSVIIKIPFQAQK-KEVFVPDN 59

Query: 60  AVPREEYTLIIRQYNIGITRLFLGFGEYELTDQSE-MLQFSERIRRVPLSVEKQGGKWIL 118
           +  ++ Y + ++ Y+  I R  + FG   + D +  M++++  +++  L V K    W +
Sbjct: 60  SKEKKYYYMEVKAYDDAIVRCSISFGGKFMEDNNNPMIEWAPSLKQEKLYVIKNKNGWDI 119

Query: 119 FTQDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGL 178
              +   R  +N  +  + +WS L P+PQ   +  ++PDG   +   A D F+P   + +
Sbjct: 120 VDDNKVVRMKVNNIKKPVRKWSNLHPEPQYFFNAKIFPDGIIAVSFLANDTFTPGIVESV 179

Query: 179 PIAFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYK 238
            + + +  GK +R   +  S  +E FAGTGERF  M+L+G+T+ L+N D  GVNNRR YK
Sbjct: 180 SLGYVEHDGKADRCVFALHSEYNEKFAGTGERFAPMNLAGKTIILENNDALGVNNRRAYK 239

Query: 239 NIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYR 298
           N+PFY+SS+ YG    T AH +LSLA  STR+VQ L +  +LD F I G   E I+  YR
Sbjct: 240 NVPFYISSKGYGLLIMTSAHVRLSLADISTRAVQALIEDDVLDLFFIGGGEPERIIYNYR 299

Query: 299 DLTGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCE 358
            +TG+P   P WS+G+WMSRM+YFSA+E  ++  ++R   +PCDVIHLDTGWF+ DW C+
Sbjct: 300 RITGFPRKVPAWSYGIWMSRMSYFSAEETLDVAKKLRENGFPCDVIHLDTGWFKKDWQCD 359

Query: 359 WKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDG 418
           W+F+EERFP+P+ +I+ + K G+++S+WQLP VA + +    A  N++I+ +TK  +   
Sbjct: 360 WEFDEERFPNPQEYIKNMHKMGFKISVWQLPQVAAETKHYNVAIENKFISRITKMSEEST 419

Query: 419 SNFSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELL 478
           SNF  ++Y G IDFT PKA +WY+ LLK L D+GV  IKTDFGENI M+A Y  M+P+ L
Sbjct: 420 SNFGDVEYRGVIDFTNPKAVKWYQNLLKNLFDLGVDVIKTDFGENIDMNAEYFSMEPKKL 479

Query: 479 NNLYALLYQKAAYEITKEVTGDG--IVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKG 536
           +N+Y+LLYQKAA+EIT+EV G G  I+WARA W GCQRYP+HWGGDS S+WDG+A +++G
Sbjct: 480 HNIYSLLYQKAAFEITEEVKGKGQAIIWARAGWIGCQRYPVHWGGDSSSTWDGLAATIRG 539

Query: 537 GLHFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWH 596
           GLH G+SGF FWSHDVPGFH LP+FMN+   +D+Y+RWTQ  VFTSHIRYHGT+ REP++
Sbjct: 540 GLHLGVSGFGFWSHDVPGFHGLPDFMNNWPDDDIYVRWTQVAVFTSHIRYHGTSPREPYN 599

Query: 597 YPAIAPLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFG 656
           YP ++ ++++WWKLRY+LIPY +EQ +   ++G+P ++AL++HHP+D+ CW+IDDE+Y G
Sbjct: 600 YPNVSDIIREWWKLRYALIPYFVEQGEKVTKTGYPFIRALLIHHPDDEYCWYIDDEFYCG 659

Query: 657 NDFLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIP 716
           + FLVAP++NS  +R+IYLP+G W++F++GE ++G   LK+VY PLE +P+Y    + + 
Sbjct: 660 DIFLVAPIINSAGKRNIYLPKGNWIDFWSGEFIKGPILLKDVYFPLERIPIYCVAGSELK 719

Query: 717 IYPEEVNCTDEMDLGKSIALRIDHNYKGF 745
           +YP  V  T E++  K+  +  DH Y+GF
Sbjct: 720 VYPYVVQHTGEIEFDKTKIIVFDHTYRGF 748


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: 1774
Number of extensions: 80
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: 748
Length of database: 759
Length adjustment: 40
Effective length of query: 708
Effective length of database: 719
Effective search space:   509052
Effective search space used:   509052
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