GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF3716 Psest_3785 Glycosidases
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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