GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Dyadobacter tibetensis Y620-1

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Pedo557:CA265_RS14455
         (443 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  145 bits (365), Expect = 3e-39
 Identities = 125/415 (30%), Positives = 192/415 (46%), Gaps = 68/415 (16%)

Query: 28  YDME--KSHGAYIYDAKHNRTLLDFFTCFASVPLGYNHPKMINDEAFKKNLFLAALANPS 85
           YD+E  K+ G+Y++D ++    LD +   A + +G+ HP    D   +    L+ ++  S
Sbjct: 11  YDIEPVKAQGSYLWD-QNGIEYLDMYGGHAVISVGHCHP----DYVARLTEQLSKISFYS 65

Query: 86  NSDVYTQQYAQFVETFSKVGIPDYLPHAFFIAGGGLAVENAIKVAMDWKVQKNFAKGYTE 145
           NS    QQ     +  +  G PDY    F    G  A ENA+K+A     +K        
Sbjct: 66  NSVQIPQQEELATKLGTLSGYPDY--KLFLCNSGAEANENALKLASFHTGRK-------- 115

Query: 146 EKGFKVLHFERAFHGRTGYTLSLTNTLPDKTKWFAKFDWPRVAVPEVKFPLSGNNLSHAI 205
               KV+ F +AFHGRT   ++ T+                   P +  P++ N     +
Sbjct: 116 ----KVVAFTKAFHGRTAGAVAATDN------------------PSIVAPVNYNEHVSFL 153

Query: 206 QTEETSLAQIKKAIADNKDDICAIIVEPIQSEGGDNHLREEFLIQIKALADENDAFLIYD 265
              +    Q     A   +++ A+IVE IQ  GG     +EFL  ++   DE  A LI D
Sbjct: 154 PFNDIEALQ-----AGITEEVAAVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILD 208

Query: 266 EVQTGVGLTGKFWCHQHFSEKARPDILAFGKKM----QVCGILVGHKVDQVETNVFKVP- 320
            VQ G G TGKF+ HQ       PD++   K M     + G+L+  +        FK   
Sbjct: 209 SVQCGYGRTGKFFSHQF--SGIHPDMMTMAKGMGNGFPIAGVLIAPQ--------FKASF 258

Query: 321 SRINSTWGGNLVDMVRSTQILQIVEEDQLCENATKVGLYLKDQLENLSHRFDQMTNVRGR 380
             + +T+GGN +       +L I++++QL +NATK+G YL  ++E L    D    +RGR
Sbjct: 259 GLLGTTFGGNHLACAAGIAVLDIMKDEQLLDNATKIGAYLFHEIEELGGYKD----LRGR 314

Query: 381 GLL--CSFDFPTKEMRNTFIAKGLENNVMFLGCGEKTIRFRPALCIEQKHIDEGL 433
           GL+    FDFP KE+RN  +    E+++     G  T+R  P+L I QK  D+ L
Sbjct: 315 GLMIGIEFDFPVKELRNKLL---FEHHIFTGVAGAYTLRLLPSLAISQKEADQFL 366


Lambda     K      H
   0.321    0.137    0.414 

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: 431
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: 443
Length of database: 384
Length adjustment: 31
Effective length of query: 412
Effective length of database: 353
Effective search space:   145436
Effective search space used:   145436
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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 (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