GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Nitratiruptor tergarcus DSM 16512

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_084274801.1 B8779_RS01390 3-isopropylmalate dehydratase large subunit

Query= curated2:O27668
         (428 letters)



>NCBI__GCF_900176045.1:WP_084274801.1
          Length = 421

 Score =  377 bits (968), Expect = e-109
 Identities = 195/421 (46%), Positives = 280/421 (66%), Gaps = 9/421 (2%)

Query: 6   MTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERI 65
           +TEKI +E  G REV  GEI+E  +D+ + +D T+P +I+ FR+     G  ++  P+  
Sbjct: 5   ITEKIFSEHVG-REVKAGEIVECELDMIIGNDITTPISIKAFRE----SGAKKLAKPDNF 59

Query: 66  VMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIF-QNAAGICHQVLPERGFVRPGMVIV 124
            +V DH +PA  I +A   +++REFA E  + + F +   GI H +LPE+G V PG VI+
Sbjct: 60  AIVLDHFIPAKDIASANQAKISREFAYEHNLKHFFDEKDMGIEHALLPEKGLVVPGDVII 119

Query: 125 GADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVIL 184
           GADSHTCT+GA GAFATGMG+TD+A    TGK WF VP ++++  TG+ + +VY KD+IL
Sbjct: 120 GADSHTCTHGALGAFATGMGSTDLAYGMITGKNWFKVPPSIKVVYTGKLDEYVYGKDLIL 179

Query: 185 HIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA 244
            +I  IGVDGA Y+++EFTGDTIE++D+ GR ++CNMA+E GAKNGI+  +  T  ++  
Sbjct: 180 ELIRRIGVDGALYKALEFTGDTIENLDMDGRFSLCNMAIEAGAKNGIIAVDEITKAFLAD 239

Query: 245 R-TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVE--GTHIDEAFL 301
           +   RE +++ SDED++Y +    DV+ LEP +A P    N  P+         +D+ F+
Sbjct: 240 KDLAREPKIHYSDEDAEYEQVIEIDVNSLEPVIAFPHLPSNGRPISEAAKMDLKVDQVFI 299

Query: 302 GSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCN 361
           GSCTNGR  D+ IAAE++  R+V    R IV+PA+++I  +A + G I+  I AGA+V N
Sbjct: 300 GSCTNGRLSDIAIAAEILKGRKVARHTRMIVTPATQKILKEAEKQGYIDILIDAGAVVSN 359

Query: 362 PGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAPQ 421
           P CG CLG +MG+LA  E  ++TTNRNF GRMG   S +YLAN AV A SA+ G I+ P+
Sbjct: 360 PTCGACLGGYMGILADNERCVSTTNRNFIGRMGARTSEIYLANSAVAAASAVAGKIADPR 419

Query: 422 Q 422
           +
Sbjct: 420 E 420


Lambda     K      H
   0.320    0.137    0.408 

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: 482
Number of extensions: 24
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: 428
Length of database: 421
Length adjustment: 32
Effective length of query: 396
Effective length of database: 389
Effective search space:   154044
Effective search space used:   154044
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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