GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Pseudomonas fluorescens FW300-N1B4

Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate Pf1N1B4_4677 Trehalose synthase (EC 5.4.99.16)

Query= curated2:Q9Z3R8
         (551 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4677
          Length = 1113

 Score =  254 bits (648), Expect = 2e-71
 Identities = 194/576 (33%), Positives = 275/576 (47%), Gaps = 113/576 (19%)

Query: 17  WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76
           W++ AVIYQ++ +SF D+N DGIGD  G+ A+L +I+ LG + IW+ PF+ SP RD GYD
Sbjct: 16  WYKDAVIYQVHVKSFFDSNNDGIGDFPGLIAKLDYISDLGVNTIWLLPFYPSPRRDDGYD 75

Query: 77  VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSR-SNAKA 135
           ++ Y  V P +GT+ D    IAEAH+ GLRV+ +LV++HTSD+H WF  +R ++  +A  
Sbjct: 76  IAEYRGVHPDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHAWFQRARKAKPGSAAR 135

Query: 136 DWYVWADS--KPDGTPPNNWLSIF---GGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190
           D+YVW+D+  K DGT       IF     S W WDP   QY+ H F + QPDLN  NPQV
Sbjct: 136 DFYVWSDNDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190

Query: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250
            +A+L+V R+WL+ G+DG RLD I  Y  +R+  +N                        
Sbjct: 191 MKAVLSVMRYWLDMGIDGLRLDAIP-YLIERDGTNN------------------------ 225

Query: 251 IYDKNRPENLEFLKRFRAVMD-EFPAIAAVGEVG----DSQRGLEIAGEYTSGGDKVHMC 305
              +N PE  + LK+ RA +D  +P    + E      D+Q            GD+ HM 
Sbjct: 226 ---ENLPETHDVLKQIRAEIDANYPDRMLLAEANQWPEDTQLYFGNTDASGQKGDECHMA 282

Query: 306 YAFEFLAPDRLT-PQRVAEVLRDFHRAAPE-----GWACWAFSNHD-----VVRHVSR-- 352
           + F  +    +   Q     + D  R  PE      WA +   NHD     +V    R  
Sbjct: 283 FHFPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDRERDY 341

Query: 353 -WADGVTDHDA-------------------HAKLLASLLMSLRGTVCIYQGEELALAEAE 392
            W     D  A                     +LL SLL+S+ GT  +Y G+E+ +    
Sbjct: 342 LWNYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMG--- 398

Query: 393 LDYEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATP----WLPISQ---SHIP 445
            D   L D            RDG RTPM W    +GGFS A P      PI      ++ 
Sbjct: 399 -DNIYLGD------------RDGVRTPMQWSIDRNGGFSRADPASLVLPPIMDPLYGYLS 445

Query: 446 RAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVE-TRGSLLGFLRSH-----GNE 499
             V  Q GDP S+L+  RR LA RK + A  +G ++ +  +   +L + R        +E
Sbjct: 446 VNVETQAGDPHSLLNWNRRLLAVRKQSKAFGRGTLKMLSPSNRRILAYTREFTGPDGKHE 505

Query: 500 KVFCLFNMSDEAATKELP------MKRLEPLEGHGF 529
            + C+ N+S  A   EL       M  +E L G+ F
Sbjct: 506 IILCVANVSRSAQAAELDLSAYVGMVPVEMLGGNAF 541


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: 1637
Number of extensions: 88
Number of successful extensions: 5
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: 1113
Length adjustment: 41
Effective length of query: 510
Effective length of database: 1072
Effective search space:   546720
Effective search space used:   546720
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