GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Pseudomonas stutzeri RCH2

Align α,α-trehalase / α-glucosidase (TTC0107) (EC 3.2.1.20|3.2.1.28) (characterized)
to candidate GFF3716 Psest_3785 Glycosidases

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



>FitnessBrowser__psRCH2:GFF3716
          Length = 511

 Score =  424 bits (1090), Expect = e-123
 Identities = 233/500 (46%), Positives = 305/500 (61%), Gaps = 47/500 (9%)

Query: 2   WWKEAVIYQVYPRSFQDTNGDGVGDLEGVRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 61
           WWK A +YQ+YPRSF D+NGDG+GDL GV R L +L+ LGVDALWLSP ++SPM D GYD
Sbjct: 9   WWKGATVYQIYPRSFADSNGDGIGDLNGVLRHLDHLQQLGVDALWLSPIFRSPMADAGYD 68

Query: 62  VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 121
           ++DYCD+DP+FG+L D DRL+ EAHA  ++VL+D VPNHTS EHPWF+ESR+SR++PKRD
Sbjct: 69  ISDYCDIDPLFGSLADIDRLIAEAHARNIRVLLDFVPNHTSDEHPWFVESRSSRDNPKRD 128

Query: 122 WYIWKDPAPDGGPPNNWQSFFG-GPAWTLDEATGQYYLHQFLPEQPDLNWRNPEVREAIY 180
           WYIW+D       PNNW++  G G AWT DE T QYYLH FL +QPDLNWRNPEV EA++
Sbjct: 129 WYIWRD------QPNNWRAALGAGSAWTWDEHTQQYYLHLFLAKQPDLNWRNPEVVEAMH 182

Query: 181 EVMRFWLRRGVDGFRVDVLWLLAEDLLFRDEPGNPDWRPGMWDRGRHLHIFTEDQPETYA 240
           +V+RFWL RG+DGFR+DV+    +DL F D+P            G+ L  F  DQP ++ 
Sbjct: 183 DVLRFWLDRGIDGFRIDVIHCTGKDLSFADDP--------RCQAGQPLSDF-NDQPYSHE 233

Query: 241 YVREMRQVLDEFSEPGRERVMVGEIYL-PYPQLVRYYQAG--CHLPFNFHLIFRGLPDWR 297
            +R +R+++D +  PG +R++VGE+ +    ++++YY AG   HL FNF+ +      W 
Sbjct: 234 VLRGLRKLVDSY--PG-DRMLVGEVNIRSTERVLQYYGAGDELHLAFNFNPLD---APWD 287

Query: 298 PENLARIVEEYES-LLTRWDWPNWVLGNHDQPRLASRL--GEAQARVAAMLLFTLRGTPT 354
           P      + E E  L     WP WVL NHD  R  SR    E  AR AA+LL TLRGTP 
Sbjct: 288 PVLFRTCIREVEHWLQPAGAWPTWVLSNHDNVRQRSRYRGSERAARAAAVLLLTLRGTPF 347

Query: 355 WYYGDEIGMKNGEIPPEKVQDPAALRQKDRLGEHNLPPGRDPERTPMQWDDTPFAGFSTV 414
            Y G+E+G+++  I  E   DP                GRD  R P+ W   P  G+   
Sbjct: 348 IYQGEELGLEDAHIRDEARIDPG---------------GRDGCRAPIPWQAEPPHGWQGA 392

Query: 415 EPWLPVNPDYKTRNVAAQEQDPRSMLHLVRRLIALRK-DPDLLYGAYRTYRAREGVYAYL 473
           EPWLP  PD        Q     S+  L +RL+A RK  P L +G +    +   V AY 
Sbjct: 393 EPWLPFPPDAAELAAERQTGAANSIFALYQRLLAARKASPALHHGDFEELASHPEVLAYR 452

Query: 474 RGEG---WLVALNLTEKEKA 490
           R  G    LV +N +E+  A
Sbjct: 453 RQHGDDCRLVCINFSEQPHA 472


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: 1037
Number of extensions: 57
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: 511
Length adjustment: 35
Effective length of query: 493
Effective length of database: 476
Effective search space:   234668
Effective search space used:   234668
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.

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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