GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacZ in Paraburkholderia bryophila 376MFSha3.1

Align β-glycosidase (β-gly) (EC 3.2.1.21|3.2.1.23) (characterized)
to candidate H281DRAFT_01455 H281DRAFT_01455 beta-glucosidase

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_01455 H281DRAFT_01455
           beta-glucosidase
          Length = 464

 Score =  398 bits (1023), Expect = e-115
 Identities = 212/426 (49%), Positives = 273/426 (64%), Gaps = 16/426 (3%)

Query: 6   EKFLWGVATSAYQIEGATQEDGRGPSIWDAFARRPGAIRDGSTGEPACDHYRRYEEDIAL 65
           + FL G AT++YQIEGA  EDGR PSIWD F   PG +  G +G  ACDHY R+E D+ +
Sbjct: 26  KNFLLGAATASYQIEGAVDEDGRLPSIWDTFCATPGKVLAGDSGAVACDHYHRWESDVDM 85

Query: 66  MQSLGVRAYRFSVAWPRILPEGRGRINPKGLAFYDRLVDRLLASGITPFLTLYHWDLPLA 125
           +  LG+  YR S+AWPR++ +  G  N KGL FY RL+ RL   GIT F+TLYHWDLP  
Sbjct: 86  LVGLGLEGYRLSIAWPRVM-DANGASNRKGLDFYKRLLTRLKEKGITTFVTLYHWDLPQH 144

Query: 126 LEERGGWRSRETAFAFAEYAEAVARALADRVPFFATLNEPWCSAFLGHWTGEHAPGLRNL 185
           LE+RGGW +RETA+ FA+YA+ ++R LA  V  +ATLNEPWCSA+LG+  G HAPGL N 
Sbjct: 145 LEDRGGWLNRETAYRFADYADLMSRELAGTVDAWATLNEPWCSAYLGYGNGHHAPGLANG 204

Query: 186 EAALRAAHHLLLGHGLAVEALRAAG-ARRVGIVLNFAPAYG-----EDPEAVDVADRYHN 239
             A +A HHLLL HGLA+  LR    + + GIV N           ED  A  + +  HN
Sbjct: 205 RFATQAMHHLLLAHGLALPVLRENDPSSQKGIVANIGRGTPNSDSVEDQRAAQLFEIQHN 264

Query: 240 RYFLDPILGKGYPESPFRDPPPVP--ILSRDLELVARPLDFLGVNYYAPVRVAPGTGTLP 297
            + LDP+L   YPE+ F   P     IL  D+++++ PLDFLG+NYY    VA   G   
Sbjct: 265 AWILDPLLKGAYPEALFELWPGTEPLILGGDMQIISAPLDFLGINYYFRTNVAT-DGAHG 323

Query: 298 VRYLPPEG-PATAMGWEVYPEGLHHLLKRLGRE---VPWPLYVTENGAAYPDLWTGEAVV 353
              +P EG   T MGWEVYP+GL  LL     E   +P P+Y+TENG A  D    +  V
Sbjct: 324 FTEVPLEGVERTQMGWEVYPDGLRDLLIGFSHEYSNLP-PVYITENGMASDDT-VIDGRV 381

Query: 354 EDPERVAYLEAHVEAALRAREEGVDLRGYFVWSLMDNFEWAFGYTRRFGLYYVDFPSQRR 413
            D +R+++L+ H+ A   A + GVD+RGYF+WSLMDNFEWAFGY RRFG+ +VD+ +Q+R
Sbjct: 382 NDTQRISFLKRHLAAVDEAIKAGVDIRGYFLWSLMDNFEWAFGYERRFGIVHVDYVTQKR 441

Query: 414 IPKRSA 419
             KRSA
Sbjct: 442 TTKRSA 447


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: 607
Number of extensions: 26
Number of successful extensions: 7
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: 464
Length adjustment: 33
Effective length of query: 398
Effective length of database: 431
Effective search space:   171538
Effective search space used:   171538
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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