GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Desulfovibrio vulgaris Hildenborough

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate 206318 DVU0890 homoserine dehydrogenase

Query= uniprot:B8DRS3_DESVM
         (436 letters)



>MicrobesOnline__882:206318
          Length = 424

 Score =  680 bits (1754), Expect = 0.0
 Identities = 347/425 (81%), Positives = 379/425 (89%), Gaps = 2/425 (0%)

Query: 11  KRLVIGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPRAWPVPQGATL 70
           K LVIGMAG GTVGSGL RVL+ENRQWI ERTGR + +K +LVRDL+KPR   +P GA+L
Sbjct: 2   KPLVIGMAGCGTVGSGLLRVLEENRQWIVERTGRAVQVKHVLVRDLSKPR--DLPDGASL 59

Query: 71  TADPAVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAEDGYDLYRLAE 130
           T DPAVLTDDPE+DVLVELMGGI  P  +I+RA+E GKHVVTANKALLAEDG+ L+RLAE
Sbjct: 60  TDDPAVLTDDPEVDVLVELMGGIEKPRELIRRAIENGKHVVTANKALLAEDGFGLFRLAE 119

Query: 131 QKNVGLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMTSNGLDFATAL 190
           +K VGL++EASVAGGIPIVQTLKESLAGNRI SLVGILNGTAN+ILSEMTS GLDF TAL
Sbjct: 120 EKGVGLYYEASVAGGIPIVQTLKESLAGNRITSLVGILNGTANHILSEMTSAGLDFETAL 179

Query: 191 AQAQELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAGIDRMDIEFAR 250
           AQAQELGYAEADPTLDI+GHDTAHKLVLLIRLAYG++YPYAE+PVQGI GIDRMDIEFAR
Sbjct: 180 AQAQELGYAEADPTLDIDGHDTAHKLVLLIRLAYGLEYPYAEMPVQGIRGIDRMDIEFAR 239

Query: 251 ELGFRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNAVGPVFLHGLG 310
           E GFRIKLL QVREVDG+LEAGVFPTLV+HT+LIARVGGAYNAIR+EGNAVGPVFLHG G
Sbjct: 240 EFGFRIKLLGQVREVDGRLEAGVFPTLVRHTYLIARVGGAYNAIRIEGNAVGPVFLHGQG 299

Query: 311 AGSLPTASAVLADLMTVARGAAPHNTGFQRQVPPRADILPPADAESSYYVRAMVPDNPGV 370
           AGSLPTAS+VLADLM VAR   PHNTGFQRQVPP+A ILPP DA S+YYVR MVPD+PGV
Sbjct: 300 AGSLPTASSVLADLMAVARATPPHNTGFQRQVPPKASILPPDDAVSAYYVRVMVPDHPGV 359

Query: 371 LRDLAGAMADHSISIAQAIQKGQHPQGVPLVFMTHAAKASAIQGAIAQVQAAGLLLAPPV 430
           LRDLAGAMADH ISIAQAIQKGQ  +GVPLVFMTH A A AI  AI Q++ AGLL A PV
Sbjct: 360 LRDLAGAMADHGISIAQAIQKGQDKRGVPLVFMTHEAGARAISDAIEQIRQAGLLTADPV 419

Query: 431 CYRVL 435
           CYRVL
Sbjct: 420 CYRVL 424


Lambda     K      H
   0.319    0.137    0.394 

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: 701
Number of extensions: 21
Number of successful extensions: 2
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: 436
Length of database: 424
Length adjustment: 32
Effective length of query: 404
Effective length of database: 392
Effective search space:   158368
Effective search space used:   158368
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 (21.7 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

Related tools

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