Aligments for a candidate for susB in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for susB in Pseudomonas stutzeri RCH2

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate GFF3716 Psest_3785 Glycosidases

Query= BRENDA::Q5SL12
         (529 letters)



>lcl|FitnessBrowser__psRCH2:GFF3716 Psest_3785 Glycosidases
          Length = 511

 Score =  430 bits (1105), Expect = e-125
 Identities = 236/500 (47%), Positives = 305/500 (61%), Gaps = 47/500 (9%)

Query: 3   WWQRAVIYQVYPRSFQDTNGDGVGDLEGIRRRLPYLKSLGVDALWLSPFYKSPMKDFGYD 62
           WW+ A +YQ+YPRSF D+NGDG+GDL G+ R L +L+ LGVDALWLSP ++SPM D GYD
Sbjct: 9   WWKGATVYQIYPRSFADSNGDGIGDLNGVLRHLDHLQQLGVDALWLSPIFRSPMADAGYD 68

Query: 63  VADYCDVDPVFGTLQDFDRLLEEAHALGLKVLVDLVPNHTSSEHPWFLESRASRNSPKRD 122
           ++DYCD+DP+FG+L D DRL+ EAHA  ++VL+D VPNHTS EHPWF+ESR+SR++PKRD
Sbjct: 69  ISDYCDIDPLFGSLADIDRLIAEAHARNIRVLLDFVPNHTSDEHPWFVESRSSRDNPKRD 128

Query: 123 WYIWKDPAPDGGPPNNWQSFFG-GPAWTLDEATGQYYLHLFLPEQPDLNWRNPEVREAIK 181
           WYIW+D       PNNW++  G G AWT DE T QYYLHLFL +QPDLNWRNPEV EA+ 
Sbjct: 129 WYIWRD------QPNNWRAALGAGSAWTWDEHTQQYYLHLFLAKQPDLNWRNPEVVEAMH 182

Query: 182 EVMRFWLRRGVDGFRVDVLWLLGKDPLFRDEPGSPLWRPGLPDRARHEHLYTEDQPETYA 241
           +V+RFWL RG+DGFR+DV+   GKD  F D+P     +P L D          DQP ++ 
Sbjct: 183 DVLRFWLDRGIDGFRIDVIHCTGKDLSFADDPRCQAGQP-LSD--------FNDQPYSHE 233

Query: 242 YVREMRQVLDEFSEPGRERVMVGEIYL-PLPRLVRYYAAG--CHLPFNFSLVTEGLSDWR 298
            +R +R+++D +  PG +R++VGE+ +    R+++YY AG   HL FNF+ +    + W 
Sbjct: 234 VLRGLRKLVDSY--PG-DRMLVGEVNIRSTERVLQYYGAGDELHLAFNFNPLD---APWD 287

Query: 299 PENLARIVETYEGLLS-RWDWPNWVLGNHDQPRLASRL--GEPQARVAAMLLFTLRGTPT 355
           P      +   E  L     WP WVL NHD  R  SR    E  AR AA+LL TLRGTP 
Sbjct: 288 PVLFRTCIREVEHWLQPAGAWPTWVLSNHDNVRQRSRYRGSERAARAAAVLLLTLRGTPF 347

Query: 356 WYYGDELALPNGLIPPEKVQDPAALRQRDREPTAYHTLGRDPERTPMPWDASPYGGFSTV 415
            Y G+EL L +  I  E   DP                GRD  R P+PW A P  G+   
Sbjct: 348 IYQGEELGLEDAHIRDEARIDPG---------------GRDGCRAPIPWQAEPPHGWQGA 392

Query: 416 EPWLPLNPDYRTRNVAAQEKDPRSMLHLVKRLIALRK-DPDLLYGAYRTYRAREGVYAYL 474
           EPWLP  PD        Q     S+  L +RL+A RK  P L +G +    +   V AY 
Sbjct: 393 EPWLPFPPDAAELAAERQTGAANSIFALYQRLLAARKASPALHHGDFEELASHPEVLAYR 452

Query: 475 RGEG---WLVALNLTEKEKA 491
           R  G    LV +N +E+  A
Sbjct: 453 RQHGDDCRLVCINFSEQPHA 472


Lambda     K      H
   0.320    0.141    0.462 

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: 1062
Number of extensions: 59
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: 529
Length of database: 511
Length adjustment: 35
Effective length of query: 494
Effective length of database: 476
Effective search space:   235144
Effective search space used:   235144
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources