GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Escherichia coli BW25113

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 14218 b0072 isopropylmalate isomerase large subunit (NCBI)

Query= curated2:Q8TLF1
         (424 letters)



>FitnessBrowser__Keio:14218
          Length = 466

 Score =  262 bits (670), Expect = 1e-74
 Identities = 171/465 (36%), Positives = 242/465 (52%), Gaps = 57/465 (12%)

Query: 14  TISEKIFSRAAGTEAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPF 73
           T+ EK+F      EA+ N+  L  +D  + H+ TS  A +  +      V  P +     
Sbjct: 4   TLYEKLFDAHVVYEAE-NETPLLYIDRHLVHEVTSPQAFDGLRA-HGRPVRQPGKTFATM 61

Query: 74  DHIAP-------ANNETSATLQREIREWVKEQGIPNFYEVG---EGICHQVLPENGFALP 123
           DH          A  E +    +E+ +  KE G+   Y++    +GI H + PE G  LP
Sbjct: 62  DHNVSTQTKDINACGEMARIQMQELIKNCKEFGV-ELYDLNHPYQGIVHVMGPEQGVTLP 120

Query: 124 GKLVVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYA 183
           G  +V  DSH+ T+GAFGA A G+G +++  + AT  L     ++ ++ V+G    G+ A
Sbjct: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180

Query: 184 KDLTLYLIGKTGIAGATYKAVEFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTF 243
           KD+ L +IGKTG AG T   VEF G+AIR+L++ GRMTLCNMAIEMGAK G+V PDE TF
Sbjct: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240

Query: 244 EFLKNR-----------AAATYEPVYADPDAVYLEEFTYDADDIEPQVAC---PHQV--- 286
            ++K R           A A ++ +  D  A +    T  A++I PQV     P QV   
Sbjct: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300

Query: 287 -DNV------------------------KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAA 321
            DN+                        KP   +    +D+VFIG+CTN R+EDL  AA 
Sbjct: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360

Query: 322 VLKGKQVA--VRTIVIPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGE 379
           + KG++VA  V+ +V+P S      A   G  +  ++AG     PGC  CL  +   L  
Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420

Query: 380 GEVCVSTANRNFKGRMGKGGFIYLASPATAAASALTGEITDPRTV 424
           GE C ST+NRNF+GR G+GG  +L SPA AAA+A+TG   D R +
Sbjct: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465


Lambda     K      H
   0.318    0.135    0.400 

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: 507
Number of extensions: 22
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: 424
Length of database: 466
Length adjustment: 32
Effective length of query: 392
Effective length of database: 434
Effective search space:   170128
Effective search space used:   170128
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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