GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Pseudomonas fluorescens FW300-N2E3

Align Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate AO353_22940 AO353_22940 alpha-amylase

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



>FitnessBrowser__pseudo3_N2E3:AO353_22940
          Length = 1113

 Score =  251 bits (640), Expect = 1e-70
 Identities = 185/557 (33%), Positives = 263/557 (47%), Gaps = 102/557 (18%)

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

Query: 68  VADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA- 126
           +A+YRGV   +GTL D  R +   H RG+RV+ + V+NH+SDQHPWF  +R ++    A 
Sbjct: 76  IAEYRGVHRDYGTLTDAKRFIAEAHNRGLRVITELVINHTSDQHPWFQRARKAKPGSAAR 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 QDQLLDDMEFWLKLGVDGFRLDAANFYF-HDAELRDNPPNTEIREGSIGVRIDNPYAYQR 240
              +L  M +WL LG+DG RLDA  +    D    +N P T      I   ID  Y    
Sbjct: 191 MKAVLSVMRYWLDLGIDGLRLDAIPYLIERDGTNNENLPETHAVLKQIRAEIDAHY---- 246

Query: 241 HIYDKTRPENMDFLRRLRALLQRYPGASSVAEIGCDESLRTMAAYTSGGDTLHMAYSFDL 300
                  P+ M     L A   ++P          D  L     +   GD  HMA+ F L
Sbjct: 247 -------PDRM-----LLAEANQWPE---------DTQLYFGDVHGDNGDECHMAFHFPL 285

Query: 301 LTE--QCSPGYIRHTVEGIERELAD-----GWSCWSMGNHDVVR---------------- 337
           +           R  +  I R+  +      W+ + + NHD +                 
Sbjct: 286 MPRMYMALAQEDRFPITDILRQTPEIPANCQWAIF-LRNHDELTLEMVTDKERDYLWNYY 344

Query: 338 -----------VMTRWALNGRPDPERGRLLMALLLSLRGSVCMYQGEELGLPEAELRYED 386
                      +  R A     D  R  LL +LLLS+ G+  +Y G+E+G+ +  +   D
Sbjct: 345 AADRRARINLGIRRRLAPLMERDRRRVELLNSLLLSMPGTPTLYYGDEIGMGD-NIYLGD 403

Query: 387 LVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGSQP----WLPVDD---SHRSLSVA 439
                          RDG RTPM W  +  + GF+ + P      P+ D    + S++V 
Sbjct: 404 ---------------RDGVRTPMQWSID-RNGGFSRADPASLVLPPIMDPLYGYLSVNVE 447

Query: 440 AQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDD-ALLVFERR-LGD----EAWLC 493
            Q  DPHS+LN  RR L  R++ +    G + M+   +  +L + R   GD    E  LC
Sbjct: 448 TQAGDPHSLLNWTRRMLAIRKQSKAFGRGSLKMLSPSNRRILAYTREYTGDDGKHEIILC 507

Query: 494 LFNLGDLSRSYELPAQA 510
           + N+   +++ EL   A
Sbjct: 508 VANVSRSAQAAELDLSA 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: 1678
Number of extensions: 93
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 542
Length of database: 1113
Length adjustment: 41
Effective length of query: 501
Effective length of database: 1072
Effective search space:   537072
Effective search space used:   537072
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