GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Caldicellulosiruptor kronotskyensis 2002

Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate WP_041742016.1 CALKRO_RS12150 alpha-glucosidase

Query= CAZy::CAA54266.1
         (587 letters)



>NCBI__GCF_000166775.1:WP_041742016.1
          Length = 555

 Score =  745 bits (1923), Expect = 0.0
 Identities = 353/567 (62%), Positives = 432/567 (76%), Gaps = 12/567 (2%)

Query: 17  IRRAWWKEAVVYQIYPRSFMDSNGDGIGDLRGILSKLDYLKLLGVDVLWLNPIYDSPNDD 76
           + + WWKEAVVYQIYPRSF DSNGDGIGDL GI+ KLDYL+ LGVDV+WLNPIY SPN D
Sbjct: 1   MHKKWWKEAVVYQIYPRSFYDSNGDGIGDLPGIIEKLDYLQELGVDVIWLNPIYKSPNAD 60

Query: 77  MGYDIRDYYKIMEEFGTMEDFEELLREVHARGMKLVMDLVANHTSDEHPWFIESRSSRDN 136
            GYDI DYY IM+EFGTMEDF+ LL E H RG+K+VMDLV NHTSDEH WF+ESR S+DN
Sbjct: 61  NGYDISDYYDIMDEFGTMEDFDRLLNEAHKRGIKIVMDLVVNHTSDEHKWFLESRKSKDN 120

Query: 137 PYRDWYIWRDPKDGREPNNWLSYFSGSAWEYDERTGQYYLHLFSRRQPDLNWENPKVREA 196
           PYRD+Y WR  K+G  PNNW S+FSG AW+YDE TG+YYLHLF+ +QPDLNW NP+VR+ 
Sbjct: 121 PYRDFYFWRPGKNGGPPNNWTSFFSGPAWKYDELTGEYYLHLFAVKQPDLNWNNPQVRQE 180

Query: 197 IFEMMRFWLDKGIDGFRMDVINAIAKAEGLPDAPARPGERYAWGGQYFLNQPKVHEYLRE 256
           I++MM++WLDKGIDGFRMDVIN I+K EGLPD P    +    G +Y+ N P+VHEYL+E
Sbjct: 181 IYKMMKWWLDKGIDGFRMDVINLISKVEGLPDDPDE-NQGGLIGFKYYANGPRVHEYLQE 239

Query: 257 MYDKVLSHYDIMTVGETGGVTTKDALLFAGEDRRELNMVFQFEHMDIDATDGDKWRPRPW 316
           M  +VLS YDIMTVGET  VT + A L+   DR ELNM+F FEHMD+D + G KW  +PW
Sbjct: 240 MNREVLSKYDIMTVGETPFVTPEIAKLYVEYDRNELNMIFHFEHMDMDCS-GSKWNIKPW 298

Query: 317 RLTELKTIMTRWQNDLYGKAWNSLYWTNHDQPRAVSRFGNDGPYRVESAKMLATVLHMMQ 376
           +LT+LK IM +W   L  K WNSLY  NHDQPR VSRFGND  YRVESAK+LAT+LH  Q
Sbjct: 299 KLTDLKKIMFKWYLALKDKGWNSLYLNNHDQPRMVSRFGNDKEYRVESAKLLATLLHTWQ 358

Query: 377 GTPYIYQGEEIGMTNCPFDSIDEYRDVEIHNLWRHRVMEGGQDPAEVLRVIQLKGRDNAR 436
           GTPYIYQGEEIGMTNC F+S DE+RD+E  N W   + + G+   E+L ++  + RD+AR
Sbjct: 359 GTPYIYQGEEIGMTNCKFESFDEFRDIETLN-WYKEMKKLGKSDEELLEILNKRSRDHAR 417

Query: 437 TPMQWDDSPNAGFTTGTPWIKVNPNYREINVKQALADPNSIFHYYRRLIQLRKQHPIVVY 496
           TPMQWDDS NAGFT GTPWIKVNPNY+EINVK+AL D NS+F+YY++LI+LRK+HP++VY
Sbjct: 418 TPMQWDDSKNAGFTKGTPWIKVNPNYKEINVKKALEDKNSVFYYYKKLIELRKKHPVIVY 477

Query: 497 GKYDLILPDHEEIWAYTRTLGDERWLIVANFFGGTPEFELPPEVRCEGAELVIANYPVDD 556
           G   ++  D E+I+AYTR+  DER L+V NF     EF  P E+  +  EL+I+NY +DD
Sbjct: 478 GDVQMLYEDDEKIFAYTRSYEDERLLVVMNFSEEESEFLAPNEIFTQKPELLISNYEIDD 537

Query: 557 SEAGGPAAAGAPHRFRLRPYECRVYRL 583
           +            +  L+PYE RVY++
Sbjct: 538 N---------IQEKIVLKPYESRVYKI 555


Lambda     K      H
   0.320    0.139    0.451 

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: 1347
Number of extensions: 72
Number of successful extensions: 5
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: 587
Length of database: 555
Length adjustment: 36
Effective length of query: 551
Effective length of database: 519
Effective search space:   285969
Effective search space used:   285969
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.

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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