GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Paraburkholderia bryophila 376MFSha3.1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate H281DRAFT_00993 H281DRAFT_00993 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::Q4DRT8
         (561 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00993 H281DRAFT_00993
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 497

 Score =  150 bits (379), Expect = 1e-40
 Identities = 134/440 (30%), Positives = 202/440 (45%), Gaps = 32/440 (7%)

Query: 90  KAIDTALQASRE------WSQTSFRDRAAIFLHAAHLISTKYRHELRAATMLGQSKSPFQ 143
           K +D A+ A+RE      WS+ +   R A+    A LI      EL     L   K   +
Sbjct: 55  KDVDRAVAAAREAFESGVWSKAAPAQRKAVLQRLAQLIDDN-AEELALLEALEAGKPISE 113

Query: 144 AEIDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEGFVSTIAPFNFAAI 203
                I ES   +R+     +  Y    LSPS  +V + +   P+ G V  + P+NF A+
Sbjct: 114 CLGLDIPESAACIRWHAEVTDKRY--DALSPSGASVVSMITREPI-GVVGAVLPWNFPAL 170

Query: 204 AANLVACPAL-MGNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFLPCEPDVMTNFVN 262
                  PAL +GN V+ KP+    LS   +  +  EAGLPAGV+N +    +     + 
Sbjct: 171 MLAWKIGPALSVGNSVIVKPAEQTSLSTLRIADLALEAGLPAGVLNVVTGFGESAGQALG 230

Query: 263 SHRDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHLVHPS-ADLKLAA 321
            H D+  VAFTGST+       + + R     N+ R+  E GGK+  +V P  A+L   A
Sbjct: 231 RHADVDLVAFTGSTE-----TGKRFLRYSADTNLKRVVLECGGKNPQVVLPDVANLDAVA 285

Query: 322 ALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDDFKSFMCAVIDE 381
              V  AF   G+ CSA SR+  P S    L   +L V E  K G P D    + ++I+E
Sbjct: 286 EQAVAAAFWNMGENCSAGSRILVPSSLKASLLEKVLAVLEVWKTGDPLDPDVKLGSLIEE 345

Query: 382 TAFERNKKYIDIAKSSPSTYSVIAGGGYDKTE--GWFVQPTIVESKDSQAQLMHEEIFGP 439
             FE+   +I+ A++  +   ++ GG   +T+  GWFV+PTI ++   Q ++  +E+FGP
Sbjct: 346 MHFEKVLAHIEKARAEGA--RLVCGGKATRTDSGGWFVEPTIFDNVTPQMRIARDEVFGP 403

Query: 440 ILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLRYAAGNYYIN 499
           ++    Y D       D    +   T Y L  S++  +   +  A     R  AG   +N
Sbjct: 404 VVCFIEYAD------IDEAVHIANDTCYGLAASLWTDN---VNHAHKIAARIRAGTVTVN 454

Query: 500 DKCTGAVVGQQPFGGARASG 519
             C G      PFGG + SG
Sbjct: 455 --CFGEGDLSTPFGGFKQSG 472


Lambda     K      H
   0.320    0.133    0.402 

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: 591
Number of extensions: 29
Number of successful extensions: 4
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: 561
Length of database: 497
Length adjustment: 35
Effective length of query: 526
Effective length of database: 462
Effective search space:   243012
Effective search space used:   243012
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 (21.8 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