GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Echinicola vietnamensis KMM 6221, DSM 17526

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate Echvi_2850 Echvi_2850 Glycosidases

Query= CAZy::AAS80455.1
         (528 letters)



>FitnessBrowser__Cola:Echvi_2850
          Length = 519

 Score =  221 bits (564), Expect = 4e-62
 Identities = 164/521 (31%), Positives = 255/521 (48%), Gaps = 90/521 (17%)

Query: 2   WWKEA-VIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGY 60
           +W EA + Y+++ +SF DT+GDG+GD+ GV ++L +++ LG +A+W  P   SP     Y
Sbjct: 33  YWPEAGITYEIFIQSFYDTDGDGIGDINGVTKKLDHVQELGANAIWFMPLMPSPSYH-KY 91

Query: 61  DVADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKR 120
           DV DY  + P +GT+ DF ++L+EAH   +KV++D++ NHTS EHPWF E++  R++P R
Sbjct: 92  DVTDYKAIHPDYGTMDDFKQMLDEAHKRDIKVVIDMIINHTSDEHPWFQEAKKGRDNPYR 151

Query: 121 DWYIWKDPAPDGGPPNNWQSFFGGPAWTLDEAT-------GQ---YYLHQFLPEQPDLNW 170
           D+Y+W          +  Q +      TLD          GQ   YY   F  + PDLN+
Sbjct: 152 DYYVW-------AQYDTIQDYLDKKVVTLDSDNIRQWHDPGQGDDYYYGFFTGDMPDLNF 204

Query: 171 RNPEVREAIYEVMRFWLRR-GVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLH 229
            NP+VRE IYE+ R+WL   GVDGFR+D    +  D                 DR    H
Sbjct: 205 DNPKVREEIYEIGRYWLAEVGVDGFRLDAAKHIYPD-----------------DRAADSH 247

Query: 230 IFTEDQPETYAYVREMRQVLDEFSEPGRERVMVGEIYLPYPQLVRYYQAGCHLPFNFHLI 289
            F E+      +  EM +V  +         +VGE+Y    ++V  Y  G    FNF   
Sbjct: 248 EFWEE------FRAEMEKVKPDV-------YLVGEVY-DMKEVVAPYLTGLRALFNFDFH 293

Query: 290 FRGLPDWRPENLARIVEEYESLLTRWDW------PNWVLGNHDQPRLASRLGEAQARV-- 341
           +  L  ++ E+   + ++   +L  ++          +  NHDQPRL + LG+++ ++  
Sbjct: 294 YTLLEAYKKEDGMLLAKKQHDILAFYNGITDDFIDATISSNHDQPRLLNELGKSKDKLKQ 353

Query: 342 AAMLLFTLRGTPTWYYGDEIGMKNGEIPPEKVQDPAALRQKDRLGEHNLPPGRDPERTPM 401
           A  +L T+ G P  YYG+EIGM  G+ P   +++P      +          +D  RT  
Sbjct: 354 AIAILMTMPGAPYIYYGEEIGML-GKKPDPNIREPFLWDVAE----------QDEGRT-- 400

Query: 402 QWDDTPFAGFSTVEPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK-DPDLLYGAY 460
           +W    F+  +TV P            +A Q++D  S  +  +R+I LR   P L  G+ 
Sbjct: 401 KWITPAFSTDNTVTP------------LAIQKEDADSYFNHYKRVIQLRNTHPALAIGSL 448

Query: 461 R--TYRAREGVYAYLRGEG---WLVALNLTEKEKALELPRG 496
                +  + V AY R  G     V  NL +K   + LP+G
Sbjct: 449 ELPAEKYPKAVMAYQRKTGEQELYVFHNLGKKSVEIPLPQG 489


Lambda     K      H
   0.321    0.141    0.466 

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: 863
Number of extensions: 55
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: 528
Length of database: 519
Length adjustment: 35
Effective length of query: 493
Effective length of database: 484
Effective search space:   238612
Effective search space used:   238612
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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