GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA 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)



>FitnessBrowser__Burk376:H281DRAFT_00993
          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 (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