GapMind for catabolism of small carbon sources

 

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

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate H281DRAFT_06542 H281DRAFT_06542 4-methylaminobutanoate oxidase (formaldehyde-forming)

Query= curated2:B8D1D7
         (357 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_06542 H281DRAFT_06542
           4-methylaminobutanoate oxidase (formaldehyde-forming)
          Length = 826

 Score =  153 bits (386), Expect = 2e-41
 Identities = 111/353 (31%), Positives = 179/353 (50%), Gaps = 29/353 (8%)

Query: 2   KKTPLFEIHKELGARLIEFHGWSM-----PVQYTSIIE--------------EHKAVRNQ 42
           +++PL+ + +E GA      GW       P +  + I+              EH+A R +
Sbjct: 431 RRSPLYALLREDGACFGSKMGWERANFFAPTRDEARIDYAFGQQNWLPLSGAEHRACRER 490

Query: 43  CGLFDVSHMGEILVEGPGALESLQKIVTNNVARLKKGQVLYTPMCKDDGGIIDDLLVYCL 102
             LFD++   + LV+G  A   LQ +V N+V  +  G  +YT M  + G    D  +  L
Sbjct: 491 VALFDMTSFSKFLVKGRDAQSVLQNLVANDVD-VPPGTTVYTGMLNERGNYESDFTLTRL 549

Query: 103 GQDKYLMVVNASNIEKDFNWVRDNSNQRTE---VVNESDNYALLALQGPNSKKILEKVSS 159
             D+YL+V   +   +DF+ + D +  R +   +V+ +  YA+LA+ GP S+++L+ VS 
Sbjct: 550 AADQYLLVTGTAQTTRDFDMI-DKAIPRDKHCVLVDVTSQYAVLAVMGPRSRELLQSVSK 608

Query: 160 VNL--DSLKFYNFTTGTLKGAEVLISRTGYTGELGYELYLSPDKAVEVWQALMEAGSDLG 217
            +   +S  F       +  A V  +R  Y GELG+ELY+  + AV V++ L EAG   G
Sbjct: 609 ADWRNESFAFGQSREVDIGYATVRATRLTYVGELGWELYVPVEFAVGVYEILHEAGKAFG 668

Query: 218 LIPAGLGARDTLRLEKGYCLYGNDIDENTHPLEAGLGWTVKFD-KASFIGKRALLKYKEE 276
           L+ AG  A D+LR+EKGY  +G ++  +T+P EA L +  K D    F G+ AL + + +
Sbjct: 669 LVNAGYYAIDSLRIEKGYRAWGRELTPDTNPFEAALAFACKLDTDIPFRGRDALAELRGK 728

Query: 277 GLSRKLVGFKLKGRG--IPRHGYPIKDNGDQIGVVTSGSMSPTLSEGIGMGYV 327
            L R++V     G    +   G  I  +G  +G V+S +   TL   + MGYV
Sbjct: 729 PLRRRMVVLTADGAADRMLWGGEAILRDGKPVGFVSSAAFGHTLGCPVAMGYV 781


Lambda     K      H
   0.317    0.138    0.404 

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: 686
Number of extensions: 30
Number of successful extensions: 5
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: 357
Length of database: 826
Length adjustment: 35
Effective length of query: 322
Effective length of database: 791
Effective search space:   254702
Effective search space used:   254702
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 (21.6 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