GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Sinorhizobium meliloti 1021

Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate SMc03064 SMc03064 alpha-glucosidase

Query= uniprot:I7EUW4
         (552 letters)



>FitnessBrowser__Smeli:SMc03064
          Length = 551

 Score =  753 bits (1945), Expect = 0.0
 Identities = 353/511 (69%), Positives = 409/511 (80%), Gaps = 5/511 (0%)

Query: 10  AQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFT 69
           + +L  D DWWRGAVIYQIYPRS+QD+NGDGIGDL+GIT RLPHIA LG DAIWISPFFT
Sbjct: 8   SSLLEPDRDWWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFT 67

Query: 70  SPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESR 129
           SPM+DFGYDVS+Y DVDP+FG+L +FD L+A AHRLGLRVMIDLVLSHTSD+H WF ESR
Sbjct: 68  SPMRDFGYDVSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESR 127

Query: 130 QSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHS 189
            SR NA+ADWYVWAD +PDGTPPNNWLSIFGGSAWQWDP R QYYLHNFL SQPDLN H+
Sbjct: 128 SSRSNAKADWYVWADSKPDGTPPNNWLSIFGGSAWQWDPTRLQYYLHNFLTSQPDLNLHN 187

Query: 190 PAVQDALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNH 249
           P VQ+ALL V RFWLERGVDGFRLDTINFY+HD ELR NPAL PE+RNA+ AP+VNPYN+
Sbjct: 188 PQVQEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNY 247

Query: 250 QEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYA 309
           QEH+Y KN+PENL FL RFRA++DE+PA AAVGEVGD+QRGLEI G YT+    VHMCYA
Sbjct: 248 QEHIYDKNRPENLEFLKRFRAVMDEFPAIAAVGEVGDSQRGLEIAGEYTSGGDKVHMCYA 307

Query: 310 FELLAKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWG----LNPAAQRLF 365
           FE LA D LT  R+AEV  +  R A  GWACWAFSNHDV+RH SRW      + A  +L 
Sbjct: 308 FEFLAPDRLTPQRVAEVLRDFHRAAPEGWACWAFSNHDVVRHVSRWADGVTDHDAHAKLL 367

Query: 366 TTMMMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNG 425
            +++M LRGT CIYQGEEL L EA++ +EDLQDPYGI+FWP+FKGRDGCRTPMVWE S  
Sbjct: 368 ASLLMSLRGTVCIYQGEELALAEAELDYEDLQDPYGIQFWPDFKGRDGCRTPMVWE-SLP 426

Query: 426 SGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAE 485
            GGFS+  PWLP+S  H+  +VA QE DP ++LHHYRR +A RKA+PALA G  + +   
Sbjct: 427 DGGFSSATPWLPISQSHIPRAVAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFVETR 486

Query: 486 GNVAFFTRQDRDEVIFCAFNLGDIPAEITLP 516
           G++  F R   +E +FC FN+ D  A   LP
Sbjct: 487 GSLLGFLRSHGNEKVFCLFNMSDEAATKELP 517


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: 1113
Number of extensions: 48
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 552
Length of database: 551
Length adjustment: 36
Effective length of query: 516
Effective length of database: 515
Effective search space:   265740
Effective search space used:   265740
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: 53 (25.0 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