GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malP in Galbibacter marinus ck-I2-15

Align Maltose phosphorylase (EC 2.4.1.8); Trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate WP_008992569.1 I215_RS13630 glycoside hydrolase family 65 protein

Query= reanno::Pedo557:CA265_RS24655
         (772 letters)



>NCBI__GCF_000300875.1:WP_008992569.1
          Length = 768

 Score =  945 bits (2442), Expect = 0.0
 Identities = 448/766 (58%), Positives = 577/766 (75%), Gaps = 5/766 (0%)

Query: 2   KNYIKADEWNIIEEGFDPHLNKISESIFSLGNGRMGQRANFEETYTGETLPGNYVAGVYY 61
           ++YIK +EW++IEEGF+P   K SES+FSLGNG MGQRANFEE Y+GE+  G+Y+AGVYY
Sbjct: 3   QDYIKPNEWSLIEEGFNPQKVKSSESLFSLGNGAMGQRANFEEDYSGESFQGSYIAGVYY 62

Query: 62  PDKTRVGWWKNGYPEYFAKVLNAANWIGIEVKLDGEILDLATA-EVSDFKRVLNMHAGYL 120
           PDKTRVGWWKNGYPEYFAKVLNA NWIGI V+++GE LDL T  +VSD+ R LNM  G+ 
Sbjct: 63  PDKTRVGWWKNGYPEYFAKVLNAPNWIGIHVQVEGETLDLNTCTKVSDYARELNMKQGWY 122

Query: 121 ERTFTAKLKSGKTLKVKSTRFCSIADDEVGAIRYSITPLNFDGRLTLMPFIDGDVKNQDS 180
           +R+F A + +G  LKVK+TRF S+   EVGAI+Y +TPLN    + + P++DG + N+DS
Sbjct: 123 QRSFVASMPNGVDLKVKATRFLSMTLTEVGAIKYEVTPLNRSVEVVITPYVDGGITNEDS 182

Query: 181 NYDEKFWDKVADEISGTE--AYIKLRTKKTEFEVCTGSNIELYKNAEKLAINPEAVRKEK 238
           N+D+ FW    +E+S  +  AY++  T KT F+VCTG   ELY + +K+ +  E V + +
Sbjct: 183 NWDDAFWQ--INEVSSKDDFAYVRSMTNKTAFDVCTGMLNELYLDDQKVEVKGEVVSESR 240

Query: 239 FVGQTFSLEVKANEEISLVKIAANLSSENYPKESLLKETKSIIAKASAKGFDTLLKEQTE 298
            VG  ++L++   ++ +LVK A  ++S N+  E L++ ++ I+ KA   GFD LL+ Q +
Sbjct: 241 KVGLKYTLKLSQGQKATLVKFAGYVTSLNHKSEVLVEASEQILIKARNYGFDALLESQIQ 300

Query: 299 AWASKWEESDIIIEGDVSAQQAIRFNIFQLFQTYTGKDDRLNIGPKGFTGEKYGGSTYWD 358
            W + W+ +DI I+GDV AQQ IRFNIFQL QTY+GKD RLNIGPKGFTGEKYGGSTYWD
Sbjct: 301 EWDAIWQMADITIKGDVKAQQGIRFNIFQLNQTYSGKDSRLNIGPKGFTGEKYGGSTYWD 360

Query: 359 TEAYCVPFYLATAPQEVSKNLLVYRHKQLGKAIENAAKLGFKDGAALYPMVTMNGEECHN 418
           TEAYC+PFY+AT  ++V++NLL YR+ QL KAIENA KLGF DGAALYPMVTM+GEECHN
Sbjct: 361 TEAYCIPFYMATKDEKVARNLLTYRYNQLDKAIENAQKLGFTDGAALYPMVTMDGEECHN 420

Query: 419 EWEITFEEIHRNGAIAFAIFNYIRYTGDESYLSDFGLEVLIGIARFWKQRVNWSNDKQQY 478
           EWEITFEEIHRNG+I FAI+NY R+T D+SY+ + GLEV+I I+RFWKQR N+S DK QY
Sbjct: 421 EWEITFEEIHRNGSILFAIYNYTRFTADKSYIPEMGLEVMIAISRFWKQRANFSTDKNQY 480

Query: 479 VMLGVTGPNEYENNVNNNWYTNILATWCMKYATEAAEIVKTQQPEKYNSLLKSLNFDQKE 538
           V+LGVTGPNEYENNVNNNW+TN +A WCM+Y  +  E+VK    + +  ++K      +E
Sbjct: 481 VILGVTGPNEYENNVNNNWFTNYIAKWCMEYTAQTIEMVKEDYADDFARVIKKTKLSDQE 540

Query: 539 FADWADIIEKMYYPQDEKLGIFLQQDGYLDKEQTLVKDLPASERPINQKWSWDRILRSCF 598
            A W ++ E MY+P DEK  ++LQQDG+LDKE   V +L  ++RPINQKWSWDRILRS +
Sbjct: 541 VAKWLEVAENMYFPFDEKRNVYLQQDGFLDKELVPVSELSKTQRPINQKWSWDRILRSPY 600

Query: 599 IKQADVLQGLYFFEEDYDLDTLKRNFDFYEPRTVHESSLSPCVHSILAAKLNDEARAYEF 658
           IKQADVLQG YFFE+ + L+ L+R+FDFYEP TVHESSLSPCVHSI AA L+   +AY F
Sbjct: 601 IKQADVLQGFYFFEDQFSLEELERHFDFYEPYTVHESSLSPCVHSIQAAVLDRMDQAYTF 660

Query: 659 YLRTARLDLDDYNNDTEDGLHITSMAGTWMSVVEGFAGMRVREGKLQFNPFLPGKWKSFS 718
           YLRT+RLDLDDYN +  +GLHITSMAGTWMSVVEGF GMRV+   L F+P +P +W +FS
Sbjct: 661 YLRTSRLDLDDYNKEVHEGLHITSMAGTWMSVVEGFGGMRVKNDCLSFDPKIPKEWDAFS 720

Query: 719 FTIGFRGATLKINITESGISIKNNAAVDLEIGIRNQLYKLAGNTEI 764
           F + FR   LK+ ++ SG + K     +L+I I  Q   L  + +I
Sbjct: 721 FKVNFRNQILKVEVSHSGTTFKLEGDRELKILINGQSTMLQPDNKI 766


Lambda     K      H
   0.317    0.134    0.401 

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: 1803
Number of extensions: 71
Number of successful extensions: 3
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: 772
Length of database: 768
Length adjustment: 41
Effective length of query: 731
Effective length of database: 727
Effective search space:   531437
Effective search space used:   531437
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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