Alignments for a candidate for treF in Pseudomonas stutzeri RCH2

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources