GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysT in Desulfovibrio vulgaris Hildenborough

Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 208495 DVU2982 3-isopropylmalate dehydratase, large subunit, putative

Query= curated2:O27668
         (428 letters)



>MicrobesOnline__882:208495
          Length = 419

 Score =  380 bits (976), Expect = e-110
 Identities = 199/416 (47%), Positives = 266/416 (63%), Gaps = 5/416 (1%)

Query: 6   MTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERI 65
           + +KIL           G+I+  RV + + +D T+P  I++FR +    G  RV+D +R+
Sbjct: 5   LAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAM----GAKRVFDKDRV 60

Query: 66  VMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQNA-AGICHQVLPERGFVRPGMVIV 124
            +V DH  P   I AA+  ++TREFARE G+ + ++    G+ H +LPE G V PG V+V
Sbjct: 61  ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120

Query: 125 GADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVIL 184
           GADSHTCTYG  GAFATG+G+TD+A   A G+TWF VP  +R   TG    +V AKD+IL
Sbjct: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180

Query: 185 HIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA 244
            +IG IGVDGA YR++EF G  IE++DV GRMT+ NMA+E G K G+   + +TL Y   
Sbjct: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240

Query: 245 RTGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAFLGSC 304
                   +S+D  + Y  +  FDV+ + P VACP   DNV PV  V+   + +  +GSC
Sbjct: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300

Query: 305 TNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCNPGC 364
           TNGR  DL+ AA V+  R+V  DVR IV PA+  I+ +AL +G+IETF+ AG IV    C
Sbjct: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360

Query: 365 GPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420
           GPCLG HMG+LA GE +IATTNRNF+GRMG   S VYL+ PA  A SA+ GVI+ P
Sbjct: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416


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: 534
Number of extensions: 24
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: 428
Length of database: 419
Length adjustment: 32
Effective length of query: 396
Effective length of database: 387
Effective search space:   153252
Effective search space used:   153252
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 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