GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_22940 AO353_22940
           alpha-amylase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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