GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Pseudomonas fluorescens FW300-N2C3

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate AO356_01250 AO356_01250 alpha-amylase

Query= uniprot:A8LLL3
         (552 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_01250
          Length = 1114

 Score =  224 bits (571), Expect = 1e-62
 Identities = 165/520 (31%), Positives = 246/520 (47%), Gaps = 108/520 (20%)

Query: 16  DPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDF 75
           DP W++ AVIYQ++ +S+ DSN DGIGD  G++E++ YIA LGV+ IW+ PF+ SP +D 
Sbjct: 13  DPLWYKDAVIYQVHVKSYFDSNNDGIGDFPGLIEKLDYIADLGVNTIWLLPFYPSPRRDD 72

Query: 76  GYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNP 135
           GYDI++Y  + P +G++AD    I  AH   LRV+ +LV++HTSDQHPWF+ +R ++   
Sbjct: 73  GYDIAEYRGISPDYGTMADARRFIAEAHKRNLRVITELVINHTSDQHPWFQRARKAKPGS 132

Query: 136 KA-DWYVWA--DAKPDGTPPNNWLSIF---GGSGWHWDARRCQYYLHNFLTSQPDLNFHC 189
           KA D+YVW+  D K DGT       IF     S W WD    QY+ H F + QPDLNF  
Sbjct: 133 KARDFYVWSDDDHKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDN 187

Query: 190 ADVQDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNH 249
             V  A+L V R+WLD G+DG RLD I + +             E   +N          
Sbjct: 188 PQVIKAVLSVMRYWLDMGIDGLRLDAIPYLI-------------ERDGTN---------- 224

Query: 250 QRHLYSKNQPENLEFLAKFRAMME-EYPAIAAVGEVG----DAQ-YGLEILGQYTRGETG 303
                ++N PE  + L   RA ++  YP    + E      D Q Y  ++  Q   G+  
Sbjct: 225 -----NENLPETHDVLKLIRAEIDANYPDRMLLAEANQWPEDTQLYFGDVDAQGMNGDE- 278

Query: 304 VHMCYAFEFLAQEKLTAKR-----VAEVLNKVDEV-ASDGWACWAFSNHDVM-------- 349
            HM + F  + +  +   +     + ++L +  E+ A+  WA +   NHD +        
Sbjct: 279 CHMAFHFPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDK 337

Query: 350 RHVSRWDLTPGAQRGML-----------------------TLLMCLRGSVCLYQGEELGL 386
                W+     +R  +                       +LL+ + G+  LY G+E+G+
Sbjct: 338 ERDYLWNYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGM 397

Query: 387 PEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFS-------IHRPWLPVS 439
            +     D                RDG RTPM W  D  +GGFS       +  P +   
Sbjct: 398 GDNIYLGD----------------RDGVRTPMQWSIDR-NGGFSRADPASLVLPPIMDPQ 440

Query: 440 TEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDI 479
             +  + V  Q   P +LL+  RR LA R+   A  +G +
Sbjct: 441 YGYQSVNVETQAGDPHSLLNWTRRMLAVRKQSKAFGRGTL 480


Lambda     K      H
   0.321    0.138    0.451 

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: 1584
Number of extensions: 92
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 552
Length of database: 1114
Length adjustment: 41
Effective length of query: 511
Effective length of database: 1073
Effective search space:   548303
Effective search space used:   548303
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: 55 (25.8 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