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_013429624.1 CALKRO_RS02935 glycoside hydrolase family 31 protein

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



>NCBI__GCF_000166775.1:WP_013429624.1
          Length = 661

 Score =  220 bits (560), Expect = 2e-61
 Identities = 170/571 (29%), Positives = 272/571 (47%), Gaps = 71/571 (12%)

Query: 187 GKKERATLSFESRPDECFAGTGERFFK-MDLSGQTLFLKNQDGQGVNNRRTYKNIPFYLS 245
           G   R T+ FES P+E   G G+     ++L G  L L +++ Q         ++PF +S
Sbjct: 119 GGSYRLTVRFESEPNEKLYGMGQYQQPFLNLKGCALELAHRNSQS--------SVPFLVS 170

Query: 246 SRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYRDLTGYPS 305
           +  YG  ++  A  K+    + T    +++   ++D ++ AG+T  EIL  Y ++TG P 
Sbjct: 171 NIGYGFLWNNPAIGKVVFGKNITEWEAYVTK--IMDYWITAGNTPAEILEQYMEVTGTPP 228

Query: 306 MPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCEWKFNEER 365
           M P ++ G W S++ Y +A E+ +I    +  + P DVI +D  +F      +WKF+E+ 
Sbjct: 229 MMPDYAMGFWQSKLRYRNAQELMDIAYEYKKRNLPLDVIVID--FFHWPHQGDWKFDEDY 286

Query: 366 FPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYI-----APLTKQQDTDGSN 420
           +P P+  ++ L+K G  V +   P V +++E  EE  +   +      P    Q  + + 
Sbjct: 287 WPYPEKMVEELRKMGIEVMVSIWPTVEKESENYEEMFSKGLLISTDRGPRVTMQFVNDTL 346

Query: 421 FSALDYAGTIDFTYPKATEWYKGLLKQ-LLDMGVTCIKTDFGE----NIHMDAVYKGMKP 475
           F        +D T P+A E+  G +K+     G+     D  E        D     + P
Sbjct: 347 F--------VDMTNPEAREFMWGKVKENYFSKGIKMYWLDEAEPEFHKYEFDNYRYYLGP 398

Query: 476 EL-LNNLYALLYQKAAYE-ITKEVTGDGIVWARAAWAGCQRY-PLHWGGDSCSSWDGMAG 532
            L + N+Y LLY K  Y+ + KE   + I   R AWAG QRY  + W GD  S+++ +  
Sbjct: 399 CLEIGNIYPLLYAKTFYDGLKKEGIENIINLIRCAWAGSQRYGVVVWSGDIASTFESLRN 458

Query: 533 SLKGGLHFGLSGFAFWSHDVPGFH----TLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHG 588
            +  GL+  ++G  +W+ D+ GF+      P+F   I+      RW QFG F    R HG
Sbjct: 459 QVACGLNMAMAGIPWWTSDIGGFYGGDPEDPSFRELII------RWFQFGAFCPVFRLHG 512

Query: 589 TNK-------------------REPWHYPAIA-PLVKKWWKLRYSLIPYIIEQSKLAVES 628
             K                    E W Y   A  + KK+  +R  L PYI  Q  L  + 
Sbjct: 513 DRKPYIPPTSNKGGGRMGSGGPNEVWSYGEEAYEIFKKYLTIREKLKPYIKRQMLLTHKK 572

Query: 629 GWPLLQALILHHPEDKLCWHIDDEYYFGNDFLVAPVMNSENR-RDIYLPEG-QWVNFFTG 686
           G P+++ L    P D   W I+DE+ FG D L+APV+    R R +YLPEG  W  + TG
Sbjct: 573 GTPIMRPLFYDFPFDTKSWEIEDEFMFGPDILLAPVLYEGMRERTVYLPEGAYWREWETG 632

Query: 687 ERLQGGRWLKEV--YVPLEEMPVYVRENAVI 715
           +  +GG   KE+    PL  +P+++R+  V+
Sbjct: 633 KVYEGG---KEIICQAPLTTIPIFIRDGVVL 660


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: 1448
Number of extensions: 97
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: 661
Length adjustment: 39
Effective length of query: 709
Effective length of database: 622
Effective search space:   440998
Effective search space used:   440998
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: 54 (25.4 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