GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Pseudomonas putida KT2440

Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate PP_4059 PP_4059 fused trehalose synthase B/maltokinase

Query= curated2:Q9Z3R8
         (551 letters)



>FitnessBrowser__Putida:PP_4059
          Length = 1106

 Score =  246 bits (627), Expect = 4e-69
 Identities = 193/560 (34%), Positives = 267/560 (47%), Gaps = 110/560 (19%)

Query: 17  WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76
           W++ AVIYQ++ +SF D+N DGIGD  G+ ++L +IA LG + +W+ PF+ SP RD GYD
Sbjct: 16  WYKDAVIYQLHIKSFFDSNNDGIGDFAGLISKLDYIAELGVNTLWLLPFYPSPRRDDGYD 75

Query: 77  VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKA- 135
           ++ Y  V P +G++ D    IAEAH+ GLRV+ +LV++HTSD+HPWF  +R ++  +KA 
Sbjct: 76  IAEYKAVHPDYGSMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARHAKRGSKAR 135

Query: 136 DWYVWA--DSKPDGTPPNNWLSIF---GGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190
           ++YVW+  D K DGT       IF     S W WDP   QY+ H F + QPDLN  NPQV
Sbjct: 136 EFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190

Query: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250
            +A++ V RFWL+ GVDG RLD I  Y  +R+  +N                        
Sbjct: 191 LKAVIGVMRFWLDLGVDGLRLDAIP-YLIERDGTNN------------------------ 225

Query: 251 IYDKNRPENLEFLKRFRAVMD-EFPAIAAVGEVGD-SQRGLEIAGEYTSGGDKVHMCYAF 308
              +N  E  + LK  RA +D  +P    + E     +      GE    GD+ HM  AF
Sbjct: 226 ---ENLAETHDVLKAIRAEIDANYPDRMLLAEANQWPEDTRPYFGE--GDGDECHM--AF 278

Query: 309 EFLAPDRLTPQRVAE---VLRDFHRAAPE-----GWACWAFSNHD-----VVRHVSR--- 352
            F    R+      E    + D  R  PE      WA +   NHD     +V    R   
Sbjct: 279 HFPLMPRMYMALAMEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDRERDYL 337

Query: 353 WADGVTDHDA-------------------HAKLLASLLMSLRGTVCIYQGEELALAEAEL 393
           W     D  A                     +LL SLL+S+ GT  +Y G+EL +     
Sbjct: 338 WNYYAEDRRARINLGIRRRLAPLLQRDRRRIELLTSLLLSMPGTPTLYYGDELGMG---- 393

Query: 394 DYEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATPWL----PISQ---SHIPR 446
           D   L D            RDG RTPM W    +GGFS A P      PI      +   
Sbjct: 394 DNIYLGD------------RDGVRTPMQWSPDRNGGFSRADPQRLVLPPIMDPLYGYQTV 441

Query: 447 AVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIE-FVETRGSLLGFLRSH----GN-EK 500
            V  Q  DP S+L+  RR LA RK   A  +G +     +   +L ++R +    GN E 
Sbjct: 442 NVEAQSHDPHSLLNWTRRMLAVRKQQKAFGRGSLRTLTPSNRRILAYIREYTDADGNTEV 501

Query: 501 VFCLFNMSDEAATKELPMKR 520
           + C+ N+S  A   EL + +
Sbjct: 502 ILCVANVSRAAQAAELELSQ 521


Lambda     K      H
   0.321    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: 1640
Number of extensions: 84
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: 551
Length of database: 1106
Length adjustment: 41
Effective length of query: 510
Effective length of database: 1065
Effective search space:   543150
Effective search space used:   543150
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 (21.9 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