Alignments for a candidate for ams in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Pseudomonas stutzeri RCH2

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate GFF3716 Psest_3785 Glycosidases

Query= uniprot:H3K096
         (538 letters)



>FitnessBrowser__psRCH2:GFF3716
          Length = 511

 Score =  397 bits (1019), Expect = e-115
 Identities = 217/515 (42%), Positives = 293/515 (56%), Gaps = 48/515 (9%)

Query: 7   WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66
           WW+G  +YQIYPRSF DS GDG+GDLNG+   LD++  L VD +WLSP F SPM D GYD
Sbjct: 9   WWKGATVYQIYPRSFADSNGDGIGDLNGVLRHLDHLQQLGVDALWLSPIFRSPMADAGYD 68

Query: 67  VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126
           +SDY D+DP+FG+L D   L+ +AH+  ++V++D V +HTSD+HPWF ESR +R NPK D
Sbjct: 69  ISDYCDIDPLFGSLADIDRLIAEAHARNIRVLLDFVPNHTSDEHPWFVESRSSRDNPKRD 128

Query: 127 WFVWADPKPDGTPPNNWLSIFG-GSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQL 185
           W++W D       PNNW +  G GSAWT+D   QQYYLH FL  QPD+N+ +PE  +A  
Sbjct: 129 WYIWRD------QPNNWRAALGAGSAWTWDEHTQQYYLHLFLAKQPDLNWRNPEVVEAMH 182

Query: 186 DNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLS 245
           D +RFWLD G+DGFR+D ++    D    D+P    G+  +    + N            
Sbjct: 183 DVLRFWLDRGIDGFRIDVIHCTGKDLSFADDPRCQAGQPLS----DFN-----------D 227

Query: 246 RPENLDFLKDLRALMDEYPG-TTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMPH 304
           +P + + L+ LR L+D YPG    VGE+ +    ER+ +Y   GD+LH+A+ F+ L+ P 
Sbjct: 228 QPYSHEVLRGLRKLVDSYPGDRMLVGEV-NIRSTERVLQYYGAGDELHLAFNFNPLDAPW 286

Query: 305 SASYLREVI---ERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSL 361
                R  I   E + + AG AWP W  SNHD VR  +R+   E      +    +L +L
Sbjct: 287 DPVLFRTCIREVEHWLQPAG-AWPTWVLSNHDNVRQRSRYRGSE---RAARAAAVLLLTL 342

Query: 362 RGSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVE 421
           RG+  +YQGEELGL +A +  E   DP          GRDGCR P+PW      G+   E
Sbjct: 343 RGTPFIYQGEELGLEDAHIRDEARIDP---------GGRDGCRAPIPWQAEPPHGWQGAE 393

Query: 422 PWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR 481
           PWLP      ELA  RQ    N+     + LLA R++ PAL  GD   +    ++L + R
Sbjct: 394 PWLPFPPDAAELAAERQTGAANSIFALYQRLLAARKASPALHHGDFEELASHPEVLAYRR 453

Query: 482 QKGDETLLCVFNLTGQEQQTTLP------VEVASD 510
           Q GD+  L   N +  EQ    P      VE+ASD
Sbjct: 454 QHGDDCRLVCINFS--EQPHAHPHAGDWHVEIASD 486


Lambda     K      H
   0.320    0.138    0.443 

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: 984
Number of extensions: 76
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: 538
Length of database: 511
Length adjustment: 35
Effective length of query: 503
Effective length of database: 476
Effective search space:   239428
Effective search space used:   239428
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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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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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