GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Pseudomonas stutzeri RCH2

Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate GFF3068 Psest_3126 Homoserine dehydrogenase

Query= BRENDA::D8WXQ1
         (432 letters)



>FitnessBrowser__psRCH2:GFF3068
          Length = 434

 Score =  329 bits (844), Expect = 9e-95
 Identities = 176/433 (40%), Positives = 266/433 (61%), Gaps = 8/433 (1%)

Query: 1   MEAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQL 60
           M+ ++VG+ GLGTVG G   +++ + +++  + G  ++V +I  +  N K D    P  +
Sbjct: 1   MKPVKVGICGLGTVGGGTFNVLKRNAEEIARRAGRGIEVAQIATRHPNAKCDTGATP--I 58

Query: 61  TTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAAS 120
           T +  D++ +P+ID+V+E++GG    +  +LKA+   KHVVTANK L+AV+G+E+   A 
Sbjct: 59  TADIFDVVNNPEIDIVVELIGGYTLAKELVLKAIENGKHVVTANKALIAVHGNEIFAKAR 118

Query: 121 ANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVL 180
             G  + +EASVAGGIP+++++ +GLA +RI  + GI+NGT N+ILT+M + GR +E+VL
Sbjct: 119 EKGVIVAFEASVAGGIPVIKAIREGLAGNRINWLAGIINGTGNFILTEMREKGRTFEDVL 178

Query: 181 KEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGK 240
           KEAQ LGYAEADP  DVEG+DAA K+ ILA++ F + +  D    EGI R+T  D+ Y +
Sbjct: 179 KEAQALGYAEADPTFDVEGIDAAHKLTILASIAFGIPLQFDKAYTEGIARLTTTDVNYAE 238

Query: 241 QLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPG 300
            LGY +K +G+A R    +E+ V PTL+     +A+VN   NAV V G+AVG T++YG G
Sbjct: 239 ALGYRIKHLGVARRTDAGIELRVHPTLIPADRLIANVNGVMNAVMVNGDAVGSTLYYGAG 298

Query: 301 AGSLPTATAVVSDLVGVMKNMRLGVNG-----ANAVTPQYQKKLKGPDEIYSKFFLRLHV 355
           AG  PTA+AVV+DLV V + +    N      A          +       S ++LR+  
Sbjct: 299 AGMEPTASAVVADLVDVTRALTTDPNNRVPHLAFQPDSLSDHPILPISACESAYYLRIQA 358

Query: 356 KDEVGVFANITSIFSEHSVSFEKILQMPLKE-NGLAEIVLVTHQASLQDYEDILVKLRDL 414
           KD  GV A + SI SE  ++ E I+Q   +E +GL  ++LVTH+   Q  +D +  L  L
Sbjct: 359 KDHPGVLAQVASILSERGINIESIMQKEAEEQDGLVPVILVTHRVVEQRIDDAIAALEKL 418

Query: 415 NAVHEIKSSYRVE 427
           + V +     RVE
Sbjct: 419 DDVADKVVRIRVE 431


Lambda     K      H
   0.316    0.134    0.368 

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: 473
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: 432
Length of database: 434
Length adjustment: 32
Effective length of query: 400
Effective length of database: 402
Effective search space:   160800
Effective search space used:   160800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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