GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Pseudomonas simiae WCS417

Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate GFF2510 PS417_12800 alpha-amylase

Query= reanno::psRCH2:GFF856
         (542 letters)



>FitnessBrowser__WCS417:GFF2510
          Length = 1115

 Score =  249 bits (636), Expect = 4e-70
 Identities = 181/560 (32%), Positives = 264/560 (47%), Gaps = 108/560 (19%)

Query: 8   WWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGYD 67
           W++  VIYQV+ +S+FDSN DG+GD PG++ KLDYIA L V+ IWL PF+ SP +D GYD
Sbjct: 16  WYKDAVIYQVHVKSYFDSNNDGIGDFPGLIAKLDYIADLGVNTIWLLPFYPSPRRDDGYD 75

Query: 68  VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA- 126
           +A+YRGV   +GT+ D  R +   H+RG+RV+ + V+NH+SDQHPWF  +R ++    A 
Sbjct: 76  IAEYRGVHSDYGTMADAKRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKAKPGSAAR 135

Query: 127 DWYVWA--DPKPDGTVPNNWLSVF---GGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAV 181
           D+YVW+  D K DGT       +F       W+WD    QY+ H F S QPDLNF  P V
Sbjct: 136 DFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDNPQV 190

Query: 182 QDQLLDDMEFWLKLGVDGFRLDAANFYFHDAELRDNPPNTEIREGSIGVRIDNPYAYQRH 241
              +L  M +WL +G+DG RLDA  +       RD   N  +                  
Sbjct: 191 MKAVLSVMRYWLDMGIDGLRLDAIPYLIE----RDGTNNENL------------------ 228

Query: 242 IYDKTRPENMDFLRRLRALLQ-RYPGASSVAEIGC---DESLRTMAAYTSGGDTLHMAYS 297
                 PE  D L+++RA +   YP    +AE      D  L         GD  HMA+ 
Sbjct: 229 ------PETHDVLKQIRAEIDAHYPDRMLLAEANQWPEDTQLYFGDKKGDDGDECHMAFH 282

Query: 298 FDLLTE--QCSPGYIRHTVEGIERELAD-----GWSCWSMGNHDVVR------------- 337
           F L+           R  +  I R+  +      W+ + + NHD +              
Sbjct: 283 FPLMPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDKERDYLW 341

Query: 338 --------------VMTRWALNGRPDPERGRLLMALLLSLRGSVCMYQGEELGLPEAELR 383
                         +  R A     D  R  LL +LLLS+ G+  +Y G+E+G+ +  + 
Sbjct: 342 NYYAADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD-NIY 400

Query: 384 YEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQP----WLPVDD---SHRSL 436
             D               RDG RTPM W  +  + GF+ + P      P+ D    + S+
Sbjct: 401 LGD---------------RDGVRTPMQWSID-RNGGFSRADPASLVLPPIMDPQYGYPSV 444

Query: 437 SVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDD-ALLVFERRL-----GDEA 490
           +V  Q  DPHS+LN  RR L  R++ +    G + M+   +  +L + R        +E 
Sbjct: 445 NVETQAQDPHSLLNWTRRMLAVRKQSKAFGRGSLKMLSPSNRRILAYTREFTGEDGRNEI 504

Query: 491 WLCLFNLGDLSRSYELPAQA 510
            LC+ N+   +++ EL   A
Sbjct: 505 ILCVANVSRSAQAAELDLSA 524


Lambda     K      H
   0.322    0.140    0.464 

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: 1693
Number of extensions: 95
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: 542
Length of database: 1115
Length adjustment: 41
Effective length of query: 501
Effective length of database: 1074
Effective search space:   538074
Effective search space used:   538074
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