GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS28770
          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 (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