GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Methanococcus aeolicus Nankai-3

Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (uncharacterized)
to candidate WP_011973918.1 MAEO_RS06135 homoserine dehydrogenase

Query= curated2:Q58997
         (336 letters)



>NCBI__GCF_000017185.1:WP_011973918.1
          Length = 340

 Score =  448 bits (1153), Expect = e-131
 Identities = 226/337 (67%), Positives = 280/337 (83%), Gaps = 1/337 (0%)

Query: 1   MDIIIVGFGAIGKGIAKVLYDKKDYLKKNYE-EFKVVAITDSSGAAIDEDGLDLLKAIEV 59
           M II+VGFG IGKG+ K +  KKDYLK  Y  + KVVAI D SG+AID++GL+L  A+++
Sbjct: 1   MKIILVGFGVIGKGVLKAITSKKDYLKDKYGMDLKVVAICDRSGSAIDDNGLNLETALKI 60

Query: 60  KEKTGKIKNYPEKGREMSSIDVIKEVDADVVVEVTPSNLETGDPAKTHILESFKNKKHVV 119
           KE+TGKI NYPEKG ++S I+ I+ V+AD ++E+TP+N+ETG PA T++LE+FKN KHV+
Sbjct: 61  KEETGKIANYPEKGTDLSIIETIQTVEADAIIEITPTNIETGAPANTYMLEAFKNGKHVI 120

Query: 120 TANKGPLALCYKELIEEAKKHGVIFRHEASVGGAMPIINLAKETLAGNEILSIRGILNGT 179
           TANKGPLA+ +KELI+ A ++  +FR EASVGGAMPIINLA + LAGNEI  I+GILNGT
Sbjct: 121 TANKGPLAVNFKELIDCANENSKLFRFEASVGGAMPIINLANDALAGNEIFEIKGILNGT 180

Query: 180 TNYILTKMEKEGLDFETALKEAKELGIAETDPTQDIEGLDTAAKIVILANSIMGMNKTIK 239
           TNYIL+KME EGLDF+T LKEA+ELGIAET+P QDI GLDTAAKIVILANS+M  N +IK
Sbjct: 181 TNYILSKMETEGLDFDTVLKEAQELGIAETNPHQDISGLDTAAKIVILANSLMNKNVSIK 240

Query: 240 DVKVKGISRITPEALFLANKRGYTIKLIGQIKDGYLIVEPMLVPIDSPLNVKGTLNVAMF 299
           DVK++GI+RITPEA+ +ANK GYTIKLIG++ +  L V P L+PID P+NVKG+LNVAM 
Sbjct: 241 DVKLEGITRITPEAIAMANKSGYTIKLIGEVSNDKLEVGPKLIPIDDPMNVKGSLNVAML 300

Query: 300 ETDLAKEVVVVGRGAGPIETASAILSDLIHIYNSTKK 336
            TDLAKEV VVGRGAG IETASAILSD+I+IY +  K
Sbjct: 301 NTDLAKEVAVVGRGAGDIETASAILSDIIYIYENNIK 337


Lambda     K      H
   0.314    0.135    0.366 

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: 458
Number of extensions: 16
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: 336
Length of database: 340
Length adjustment: 28
Effective length of query: 308
Effective length of database: 312
Effective search space:    96096
Effective search space used:    96096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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