GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Novosphingobium barchaimii LL02

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_059152026.1 V474_RS13885 homoserine dehydrogenase

Query= reanno::Korea:Ga0059261_2711
         (430 letters)



>NCBI__GCF_001046635.1:WP_059152026.1
          Length = 435

 Score =  567 bits (1460), Expect = e-166
 Identities = 298/434 (68%), Positives = 346/434 (79%), Gaps = 5/434 (1%)

Query: 1   MTEPLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFD 60
           M EPL +ALAGLGTVG+GV+RLI+ NAELIARRA RPI I AVSARDR KDRGVD++R+D
Sbjct: 1   MVEPLNIALAGLGTVGSGVVRLIETNAELIARRARRPIRIAAVSARDRTKDRGVDLSRYD 60

Query: 61  WVDDMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQV 120
           W DD   LA     DVVVE++GGSDGPALALAR  +A GKGLVTANKAMIAHHGLELA  
Sbjct: 61  WEDDTAALAARADVDVVVEMVGGSDGPALALARNAIAGGKGLVTANKAMIAHHGLELAAA 120

Query: 121 AEKSDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGE 180
           AE +   +KFEAAVAGG+PVIKGL EGAAAN I+RVYGILNGTCN+ILS ME  GRDF +
Sbjct: 121 AEAAGVALKFEAAVAGGIPVIKGLSEGAAANAIERVYGILNGTCNYILSTMEDTGRDFAD 180

Query: 181 VLAEAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAE 240
           VLA+AQ  G+AEADP+FDI+G+DAAHKLSILA+IAFGT+  F  V   GI  + AADI +
Sbjct: 181 VLADAQRMGYAEADPTFDIEGIDAAHKLSILAAIAFGTRLRFDAVETMGISRVKAADIEQ 240

Query: 241 AAALGYRIRLLGIADLSG-NG---LFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRL 296
           A ALGY IRL+G+A + G NG   LFQRV PHLVP+ HPLAHV G TNAVVAEGNF+GRL
Sbjct: 241 ARALGYVIRLIGMAGIDGTNGSARLFQRVRPHLVPIDHPLAHVDGATNAVVAEGNFMGRL 300

Query: 297 LFQGAGAGDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTV 356
           LFQGAGAGDGPTASAVVAD+IDIA+ E GP +AMPA  L A   A +G R G +Y+RFTV
Sbjct: 301 LFQGAGAGDGPTASAVVADIIDIAKGEKGPAFAMPAAELEAMEPASSGHRVGSSYIRFTV 360

Query: 357 ADKVGVLAEIAAAMRDAGVSIESLIQRG-AMADGSVLVAIVTHEVPERSIAQALEKLRGS 415
            D+ GVLA+I AAMRDAGVSIESLIQ+G    DG V++A+VTH  PE ++ +A+  L GS
Sbjct: 361 PDRPGVLADITAAMRDAGVSIESLIQKGDPDQDGEVILAVVTHPGPESAVTEAMRILDGS 420

Query: 416 PSLAGEPMWMHILG 429
            SLAG P+ M I+G
Sbjct: 421 DSLAGRPLVMQIIG 434


Lambda     K      H
   0.319    0.136    0.388 

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: 613
Number of extensions: 20
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: 430
Length of database: 435
Length adjustment: 32
Effective length of query: 398
Effective length of database: 403
Effective search space:   160394
Effective search space used:   160394
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 26 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