GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacZ in Nocardiopsis gilva YIM 90087

Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate WP_094932864.1 CDO52_RS20930 beta-glucosidase

Query= CAZy::ABI35984.1
         (431 letters)



>NCBI__GCF_002263495.1:WP_094932864.1
          Length = 475

 Score =  429 bits (1103), Expect = e-125
 Identities = 226/453 (49%), Positives = 273/453 (60%), Gaps = 38/453 (8%)

Query: 8   FLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIALMQ 67
           F WG AT+A+QIEGAT+ DGRG SIWD FA  PG +  G TGEPA +HYRRY ED+AL++
Sbjct: 7   FAWGAATAAFQIEGATRADGRGVSIWDTFAATPGRVLGGDTGEPAANHYRRYAEDVALLR 66

Query: 68  SLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLALE 127
           SLG+  YRFS+AWPRI P+G G  NP GL FYDRLVD LLA+GI P+ TLYHWDLP  LE
Sbjct: 67  SLGIGNYRFSLAWPRIQPDGTGPGNPAGLDFYDRLVDELLAAGIEPWPTLYHWDLPQPLE 126

Query: 128 ERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNLEA 187
           + GGW +R+TA  FAEYA    R L DRV  + T+NEPW  AFLG+ +GEHAPG R   +
Sbjct: 127 DAGGWPARDTALRFAEYAAIAHRRLGDRVRTWCTINEPWVVAFLGYASGEHAPGRREPAS 186

Query: 188 ALRAAHHLLLGHGLAVEALRAAGAR---------RVGIVLNFAPAYGEDPEAVDV----- 233
           AL A HHL+LGHGLA  A+R  GA           VGIVLN  P    +    D+     
Sbjct: 187 ALAATHHLMLGHGLAAAAIRGQGATTTGTRPGTPAVGIVLNAQPIRPHEGSVADLDAARR 246

Query: 234 ADRYHNRYFLDPILGKGYPESPFRDPPPVP----ILSRDLELVARPLDFLGVNYYAPVRV 289
            D   NR FLDP+    YP+    D   V     +   DL  +A PLDFLG+NYY+P  V
Sbjct: 247 VDGVRNRIFLDPLYHGRYPDDVRADLADVSDFAFVRDGDLTTIAAPLDFLGINYYSPASV 306

Query: 290 APGTGTLPVRYLPPEG-------------------PATAMGWEVYPEGLHHLLKRLGREV 330
               G +    L P G                   P T   WE+   GL  LL RL  + 
Sbjct: 307 TGAAGKVDPELLEPAGDGPSRLVGCEDVGVLRGAEPRTDQDWEIDATGLTELLLRLAVDY 366

Query: 331 P-WPLYVTENGAAYPDLWTGEAVVEDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMD 389
           P  PLYVTENGA+Y D    +  V DP R +YL+ HV A   A   G  ++GYFVWSL+D
Sbjct: 367 PGTPLYVTENGASYRDEVADDGAVHDPRRASYLDQHVRATHAALTAGAPVKGYFVWSLLD 426

Query: 390 NFEWAFGYTRRFGLYYVDFPSQRRIPKRSALWY 422
           NFEWA+GY+ RFG+ +VD+ +QRR  K S  WY
Sbjct: 427 NFEWAYGYSERFGIIHVDYDTQRRTVKDSGRWY 459


Lambda     K      H
   0.322    0.140    0.453 

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: 690
Number of extensions: 38
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: 431
Length of database: 475
Length adjustment: 33
Effective length of query: 398
Effective length of database: 442
Effective search space:   175916
Effective search space used:   175916
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: 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