GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ascB in Tatumella morbirosei LMG 23360

Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate WP_046791705.1 HA49_RS06695 glycoside hydrolase family 1 protein

Query= CAZy::BAD77499.1
         (478 letters)



>NCBI__GCF_000757425.2:WP_046791705.1
          Length = 473

 Score =  459 bits (1181), Expect = e-134
 Identities = 232/478 (48%), Positives = 314/478 (65%), Gaps = 9/478 (1%)

Query: 1   MEHRHLKPFPPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDH 60
           M++  LKPFP GFLWGA+++AYQ+EGAWNE+GKG SV D+  + P  T   T+  VA DH
Sbjct: 1   MKYSKLKPFPSGFLWGASTSAYQIEGAWNEEGKGPSVIDMRHEYPQGT---TDFKVASDH 57

Query: 61  YHRYKEDVALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRTHGIEPIV 120
           YH+YK+D+ L++E GLKAYRFS++W+R+FP G+G +N  GL FY  LI+E+R+ G+EPIV
Sbjct: 58  YHQYKQDIRLLSETGLKAYRFSIAWTRIFPAGDGEINPAGLQFYHNLIDEIRSCGMEPIV 117

Query: 121 TLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISLGYR 180
           TLYH+D+PQ L D  G W +RR +D F RYA TLF   G +VKYW+T+NEQN+ I  G  
Sbjct: 118 TLYHFDLPQTLQDI-GGWHNRRTVDAFIRYANTLFTELGSKVKYWLTINEQNLMILQGNA 176

Query: 181 LGLHPPGVKDMKR-MYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPEN 239
           LG   P V++ K+ +Y+ NH   +A A V+++     P+  IGP+   + +Y    +PE+
Sbjct: 177 LGTVDPKVQNNKKHLYQQNHNMLVAQAAVMENLHKNHPEALIGPAPNIALIYAASPKPED 236

Query: 240 VLAFENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQEAKPDFMGVN 299
           VLA EN    +N  ++D+   G Y   AW YLE +G  P +  GD E+L   KPDF+  N
Sbjct: 237 VLASENYNAIRNWLYLDMAVSGQYNHLAWAYLEEKGYLPEIEEGDMEILSRGKPDFIAFN 296

Query: 300 YYQTTTVEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTTNWDWAIDPVGL 359
           YY T TVE +  DG  E +    G K     SG  G+ +   N ++  T +   IDPVG 
Sbjct: 297 YYTTQTVEASRGDGHDEVIRG--GNK--YLKSGEDGVHRGASNNFLPRTEFGTEIDPVGF 352

Query: 360 RIGLRRIANRYRLPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQEIQRAITDGVDV 419
           R  LR I  RY LP+LITENG+G FD  + D  +ND YRIDYLR HI+++Q AITDGV +
Sbjct: 353 RNTLRAIYGRYHLPLLITENGIGAFDKPDADGTINDQYRIDYLRSHIEQMQLAITDGVRI 412

Query: 420 LGYCVWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIATNGAE 477
           +GY  WS  DL+S   G  KRYG +YVNRD+   +DL+RI+KKS +WY++VI  NG +
Sbjct: 413 IGYTPWSAIDLISTHQGCSKRYGLIYVNRDEFDLRDLKRIRKKSSFWYEKVILNNGID 470


Lambda     K      H
   0.320    0.139    0.448 

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: 812
Number of extensions: 43
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: 478
Length of database: 473
Length adjustment: 33
Effective length of query: 445
Effective length of database: 440
Effective search space:   195800
Effective search space used:   195800
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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