GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate H281DRAFT_00993 H281DRAFT_00993 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



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

 Score =  464 bits (1194), Expect = e-135
 Identities = 231/490 (47%), Positives = 336/490 (68%), Gaps = 5/490 (1%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           W+ KA +L+++ R FI G+   AA NETF T++P T   LA IA+  + D+DRA++AAR 
Sbjct: 7   WKQKADALSLDGRAFIAGQRANAASNETFATLNPSTGKVLADIAKCDTKDVDRAVAAARE 66

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
            FE G WS ++PA+RKAVL +LA L++ +AEELALLE L+ GKPI   L  DIP +A  I
Sbjct: 67  AFESGVWSKAAPAQRKAVLQRLAQLIDDNAEELALLEALEAGKPISECLGLDIPESAACI 126

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW+AE  DK Y  ++ + +  ++MI REP+GV+ A++PWNFP L+  WK+GPAL+ GNSV
Sbjct: 127 RWHAEVTDKRYDALSPSGASVVSMITREPIGVVGAVLPWNFPALMLAWKIGPALSVGNSV 186

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           I+KP+E++ LS +R+A LA EAGLP GVLNVVTGFG  AGQAL RH D+D +AFTGST T
Sbjct: 187 IVKPAEQTSLSTLRIADLALEAGLPAGVLNVVTGFGESAGQALGRHADVDLVAFTGSTET 246

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
           GK+ L+ + D+N+KRV LE GGK+  +V  D  +L   A    A  F+N G+ C AG+R+
Sbjct: 247 GKRFLRYSADTNLKRVVLECGGKNPQVVLPDVANLDAVAEQAVAAAFWNMGENCSAGSRI 306

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+  S+    L  +    + W+ G PLDP   +G+LI+  H + V + I +  ++G  L+
Sbjct: 307 LVPSSLKASLLEKVLAVLEVWKTGDPLDPDVKLGSLIEEMHFEKVLAHIEKARAEGARLV 366

Query: 369 DGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G  A    + G    PTIF +V P   ++R+E+FGPV+    +   ++A+ +AND+ YG
Sbjct: 367 CGGKATRTDSGGWFVEPTIFDNVTPQMRIARDEVFGPVVCFIEYADIDEAVHIANDTCYG 426

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSG-NGRDKSLHALEKF 483
           L A++WT +++ AH+++ R++AG+V VN + +GD++ PFGG+KQSG  GRDKS++A +++
Sbjct: 427 LAASLWTDNVNHAHKIAARIRAGTVTVNCFGEGDLSTPFGGFKQSGFGGRDKSVYAHDQY 486

Query: 484 TELKTIWISL 493
            ELKT W+ L
Sbjct: 487 CELKTTWLKL 496


Lambda     K      H
   0.317    0.133    0.389 

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: 600
Number of extensions: 27
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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.

Links

Downloads

Related tools

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