GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Pseudomonas stutzeri RCH2

Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate GFF856 Psest_0870 Glycosidases

Query= uniprot:I7EUW4
         (552 letters)



>FitnessBrowser__psRCH2:GFF856
          Length = 542

 Score =  605 bits (1559), Expect = e-177
 Identities = 289/525 (55%), Positives = 359/525 (68%), Gaps = 15/525 (2%)

Query: 18  DWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGY 77
           +WWRG VIYQ+YPRS+ DSNGDG+GDL G+  +L +IASL VDAIW+SPFFTSPMKDFGY
Sbjct: 7   NWWRGGVIYQVYPRSFFDSNGDGVGDLPGVLHKLDYIASLNVDAIWLSPFFTSPMKDFGY 66

Query: 78  DVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARA 137
           DV+DY  VDP+FG+L +F +LV A H  G+RV+ID VL+H+SDQH WF ESR SRDN +A
Sbjct: 67  DVADYRGVDPLFGTLDDFVRLVEACHERGMRVLIDQVLNHSSDQHPWFAESRSSRDNDKA 126

Query: 138 DWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALL 197
           DWYVWADP+PDGT PNNWLS+FGG AW WD RR QYYLHNFL SQPDLNFH PAVQD LL
Sbjct: 127 DWYVWADPKPDGTVPNNWLSVFGGPAWSWDSRRRQYYLHNFLSSQPDLNFHCPAVQDQLL 186

Query: 198 DVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSV-NPYNHQEHLYSK 256
           D   FWL+ GVDGFRLD  NFY+HDAELR NP    E R  +I   + NPY +Q H+Y K
Sbjct: 187 DDMEFWLKLGVDGFRLDAANFYFHDAELRDNPP-NTEIREGSIGVRIDNPYAYQRHIYDK 245

Query: 257 NQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKD 316
            +PEN+ FL R RALL  YP  ++V E+G     L  M +YT+    +HM Y+F+LL + 
Sbjct: 246 TRPENMDFLRRLRALLQRYPGASSVAEIG-CDESLRTMAAYTSGGDTLHMAYSFDLLTEQ 304

Query: 317 VLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLN----PAAQRLFTTMMMCL 372
             +   +      ++R  A+GW+CW+  NHDV+R  +RW LN    P   RL   +++ L
Sbjct: 305 -CSPGYIRHTVEGIERELADGWSCWSMGNHDVVRVMTRWALNGRPDPERGRLLMALLLSL 363

Query: 373 RGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGFSAG 432
           RG+ C+YQGEELGLPEA++ +EDL DPYGI FWPEFKGRDGCRTPM WE      GF+  
Sbjct: 364 RGSVCMYQGEELGLPEAELRYEDLVDPYGITFWPEFKGRDGCRTPMPWESEAHHAGFTGS 423

Query: 433 KPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFFT 492
           +PWLPV   H +LSVA+Q+ADP +ML+ YRR +  R+    L  G    +  +  +  F 
Sbjct: 424 QPWLPVDDSHRSLSVAAQDADPHSMLNCYRRFLGWRREQRLLIEGDIHMVYHDDALLVFE 483

Query: 493 RQDRDEVIFCAFNLGDIPAEITLPEGTWRKPDTDIALADLPQSGA 537
           R+  DE   C FNLGD+     LP          + L D+P S A
Sbjct: 484 RRLGDEAWLCLFNLGDLSRSYELPAQA-------VPLVDVPASFA 521


Lambda     K      H
   0.321    0.137    0.444 

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: 1105
Number of extensions: 44
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: 1
Length of query: 552
Length of database: 542
Length adjustment: 36
Effective length of query: 516
Effective length of database: 506
Effective search space:   261096
Effective search space used:   261096
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: 52 (24.6 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