GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Dechlorosoma suillum PS

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate Dsui_2907 Dsui_2907 homoserine dehydrogenase

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>FitnessBrowser__PS:Dsui_2907
          Length = 436

 Score =  328 bits (840), Expect = 3e-94
 Identities = 188/425 (44%), Positives = 260/425 (61%), Gaps = 10/425 (2%)

Query: 5   LRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWVDD 64
           + V L G+GTVG G   ++  NAE I RRAGRPIEI  V+ R+    R V        DD
Sbjct: 4   INVGLLGIGTVGGGTFTVLKRNAEEITRRAGRPIEISIVADRNLDLARQVTGGACKVTDD 63

Query: 65  MTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAEKS 124
              +   P  D+VVELIGG  G A  L    +  GK +VTANKA++A HG E+   A+K 
Sbjct: 64  AFAVVSDPNVDIVVELIGGY-GVAKDLVMKAIENGKHVVTANKALLATHGNEIFAAAQKK 122

Query: 125 DTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVLAE 184
              + FEAAVAGG+P+IK LREG +AN+I+ V GI+NGT NFILS+M  +G  F +VL E
Sbjct: 123 GVIVAFEAAVAGGIPIIKALREGLSANRIEWVAGIINGTTNFILSEMRDKGLSFADVLKE 182

Query: 185 AQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAAAL 244
           AQ  G+AEADP+FD++GVDAAHKL+I+++IAFG   +F    + GI  L A DI  A  L
Sbjct: 183 AQRLGYAEADPTFDVEGVDAAHKLTIMSAIAFGIPMSFDKAHVEGITKLDAIDIKYAEQL 242

Query: 245 GYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAGAG 304
           GYRI+LLG+   +  G+  RVHP L+P    +A+V G  NAV+ +G+ VG  L+ G GAG
Sbjct: 243 GYRIKLLGVTKRTPEGVELRVHPTLIPEKRLIANVEGAMNAVLVKGDAVGATLYYGKGAG 302

Query: 305 DGPTASAVVADLIDIARTEFGPP------YAMPATSLAAEPVAPTGERRGRAYLRFTVAD 358
             PTASAV+ADL+D+ R     P       A    ++   P+ P  E +   YLR  V D
Sbjct: 303 AEPTASAVIADLVDVTRLHTSDPEHRVPHLAFQPDAVVDLPILPLAEVQTAYYLRLRVED 362

Query: 359 KVGVLAEIAAAMRDAGVSIESLIQRGAMADGSVL--VAIVTHEVPERSIAQALEKLRGSP 416
           K GVLA+I   + D  +SI+++IQ+    +G V   + ++TH+  E+++  A+ K+    
Sbjct: 363 KPGVLADITRILADQSISIDAMIQK-EPGEGEVQTDIILLTHQTREKNVDAAIAKIEALA 421

Query: 417 SLAGE 421
           ++ G+
Sbjct: 422 AVQGQ 426


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: 462
Number of extensions: 13
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: 436
Length adjustment: 32
Effective length of query: 398
Effective length of database: 404
Effective search space:   160792
Effective search space used:   160792
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.

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