GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacZ in Aquimarina macrocephali JAMB N27

Align β-galactosidase (Mbgl) (EC 3.2.1.23) (characterized)
to candidate WP_024770669.1 Z054_RS0113925 family 1 glycosylhydrolase

Query= CAZy::AEQ38581.1
         (447 letters)



>NCBI__GCF_000520995.1:WP_024770669.1
          Length = 437

 Score =  320 bits (819), Expect = 7e-92
 Identities = 167/436 (38%), Positives = 252/436 (57%), Gaps = 13/436 (2%)

Query: 15  WGVASAAYQIEGAVNEDGRSPSIWDTFSHTPGNLKTGENGDVACDFYHRYHDDIAFIREM 74
           WGVA AA+Q EGA N+DG+  SIWDTF+  P  +K   N  +A DFYHR+ +DI    ++
Sbjct: 9   WGVAIAAHQTEGAYNKDGKGLSIWDTFTQKPYRVKDRSNARIATDFYHRFEEDIDLAVDI 68

Query: 75  NMQVHRFSLAWPRILPGGTGPVNQKGLDFYHRVIDRTLELGLQPWVTLIHWDLPQCWRQG 134
            +Q+ RFS++W RI P GTG VN KG+++Y +V++  L++G++PW+T  HWDLPQ  +  
Sbjct: 69  GLQIFRFSISWSRIFPEGTGVVNPKGIEYYDKVVNYCLKVGIEPWITTYHWDLPQKLQDK 128

Query: 135 AAGTNRDICGLVSQLRGKVCSMSFGGLDQAT-WNVASRCPTVL--GYMQGTHAPGRRGFG 191
              TNR+I   +S     +  +     D+   W + +     +  GY  G HAPG++G  
Sbjct: 129 GGWTNRNI---ISWYAAYITVLRDHFADRVKHWVLINEGIVCIGGGYFLGVHAPGKKGIR 185

Query: 192 NFLPAVHHAALAQAEGGRVLRAHVPDAQIGTTFSASYVQPAGPTWLSRMAAANYDVIANR 251
           NF+ + HH  LAQAEG ++L+    + Q+GT  S + ++P         AA   D + NR
Sbjct: 186 NFISSTHHLLLAQAEGFKILK-EKKELQVGTAISCTKIEPYRNKIADHNAAIRIDTLMNR 244

Query: 252 LFLEPALGLGYPWKTTPFLLALQRYIRPGDMERLAFNFDFIGLQTYFRQLVRFDLLNPGT 311
           LF+EP LGLGYP    P L  + +Y + GDME L  +FDF G+QTY R++V+     P  
Sbjct: 245 LFIEPHLGLGYPDDDFPVLKRMSKYYKKGDMEALKTDFDFWGIQTYAREVVKAAWYVPYL 304

Query: 312 WGREVPHAERGSKELTEMGWEVWPENIYRLLKQFAAYKGVKRIIITENGAAFPDKLEGEQ 371
              +V   +R  K  + MGWE +PE +   L++FA Y   K + ++E G A       E 
Sbjct: 305 GAIQVKPEKRNVK-TSVMGWETYPEGVQYFLERFAQYNPKKTLWLSECGMAL-----SEN 358

Query: 372 VHDPQRIQFVQDHLAQVLRAKQEGVPVEGYFYWSLLDNFEWAEGYRPRFGLVYVDYPTQK 431
             D  RI++ Q  +  +     + + ++G   W+L+DNFEWAEGY P+FG++ +D  T +
Sbjct: 359 EDDQIRIEYYQRVIKGMETMLDKNINLKGILLWTLVDNFEWAEGYIPKFGIISLDRKTMQ 418

Query: 432 RVLKDSGKWFRAFLAN 447
           R +K S  W + +L+N
Sbjct: 419 RRMKKSALWLKKYLSN 434


Lambda     K      H
   0.323    0.140    0.460 

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: 641
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: 447
Length of database: 437
Length adjustment: 32
Effective length of query: 415
Effective length of database: 405
Effective search space:   168075
Effective search space used:   168075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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