GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Burkholderia phytofirmans PsJN

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase

Query= BRENDA::Q72IB9
         (516 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28770 BPHYT_RS28770 aldehyde
           dehydrogenase
          Length = 480

 Score =  275 bits (703), Expect = 3e-78
 Identities = 174/456 (38%), Positives = 256/456 (56%), Gaps = 19/456 (4%)

Query: 41  YIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100
           ++GGEWVD  +   ++NPS  S+V+G  A+A   + + A+ +A  AF+TW     + R  
Sbjct: 7   FVGGEWVDGNDFAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQQRFD 66

Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160
           LL +A + +  RK EL   L  E GK   EA  +V  A    +++A  ALR      E++
Sbjct: 67  LLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRV---GGEIL 123

Query: 161 PY--PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGA- 217
           P   PG   E    P+G   +I PWNFP+AI    I   +A GN V+ KPAE  +V G+ 
Sbjct: 124 PSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAE--LVPGSV 181

Query: 218 -KVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276
            ++ +I  EAG P GV+N + G+G  VG  LV       ++FTGS+  G  I  AA  +A
Sbjct: 182 WELVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAI--AAKCVA 239

Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336
            G    K+  +E GGK+ ++V + AD D+A E  +  A+   GQ+C+A+SRLI+T G ++
Sbjct: 240 TG----KKFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHD 295

Query: 337 PVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEG- 394
             +E +L R   L +G A + +  +GPVV A+Q  +   YIE+ +NEG  V GG+R+   
Sbjct: 296 RFVEAMLARMRSLKIGNALDASTQIGPVVDAKQLEQDERYIELARNEGGSVFGGERVTSA 355

Query: 395 -EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRK 453
            EG+F+AP + T   P   I +EE+FGPV SVI+V ++ EAL VAND+P+GL+ G+ +  
Sbjct: 356 TEGFFLAPALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMS 415

Query: 454 REHLEWARREFHVGNLYFNRKITGALVGVQPFGGFK 489
             H    +R    G +  N    G    V PFGG K
Sbjct: 416 LAHASHFKRHVQAGMVMINTATAGVDYHV-PFGGRK 450


Lambda     K      H
   0.319    0.137    0.403 

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: 633
Number of extensions: 36
Number of successful extensions: 6
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: 516
Length of database: 480
Length adjustment: 34
Effective length of query: 482
Effective length of database: 446
Effective search space:   214972
Effective search space used:   214972
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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