GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hom in Magnetospirillum magneticum AMB-1

Align Homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate WP_011386084.1 AMB_RS18865 homoserine dehydrogenase

Query= uniprot:A0A1L6J6Q3
         (430 letters)



>NCBI__GCF_000009985.1:WP_011386084.1
          Length = 428

 Score =  399 bits (1025), Expect = e-116
 Identities = 213/415 (51%), Positives = 280/415 (67%), Gaps = 2/415 (0%)

Query: 4   PLRVALAGLGTVGAGVIRLIDANAELIARRAGRPIEIVAVSARDRAKDRGVDITRFDWVD 63
           PL++A+AGLGTVG G ++L+  +A L+A RAGRP+ +V  +A  +  D  +D   F    
Sbjct: 5   PLKIAIAGLGTVGGGTVQLLHDHAPLLAARAGRPLALVGAAALAKPADLPLDGVPF--FT 62

Query: 64  DMTELARHPKADVVVELIGGSDGPALALARATLAAGKGLVTANKAMIAHHGLELAQVAEK 123
           D  ++A+    DV+VELIGG+ G AL + R  L  GK +VTANKAMIAHHG+ELA++AE 
Sbjct: 63  DARDMAKTCDYDVLVELIGGAKGIALDVVRTALERGKSVVTANKAMIAHHGIELARIAEA 122

Query: 124 SDTPMKFEAAVAGGVPVIKGLREGAAANQIDRVYGILNGTCNFILSKMEAEGRDFGEVLA 183
               + FEA+V GG+PVIK LREG A N++ +V GILNGTCN+IL+ M   GRDF +VLA
Sbjct: 123 KGGNIGFEASVGGGIPVIKSLREGLAGNRVTKVMGILNGTCNYILTTMRDSGRDFSDVLA 182

Query: 184 EAQAAGFAEADPSFDIDGVDAAHKLSILASIAFGTQPAFGDVAIGGIRHLLAADIAEAAA 243
           EAQA G+AEADPSFDIDG D AHKL+ILAS+AF        V+  GIR++ A DI  A  
Sbjct: 183 EAQALGYAEADPSFDIDGTDTAHKLAILASLAFAMPLDIDAVSCEGIRNVSALDIRYADE 242

Query: 244 LGYRIRLLGIADLSGNGLFQRVHPHLVPLSHPLAHVLGPTNAVVAEGNFVGRLLFQGAGA 303
           LGYRI+LLG+A LS  G+  RV+P +VPLS PLAHV GP NA+V EG+FVGR + +G GA
Sbjct: 243 LGYRIKLLGVASLSDQGVETRVYPAMVPLSFPLAHVSGPFNAIVTEGDFVGRTVLEGRGA 302

Query: 304 GDGPTASAVVADLIDIARTEFGPPYAMPATSLAAEPVAPTGERRGRAYLRFTVADKVGVL 363
           G  PTASAVVADL+D+A    GP + +   +L A P AP+G  R   Y+R  V D+ GV 
Sbjct: 303 GARPTASAVVADLMDLATGRVGPTFGIAVDALKALPAAPSGTHRSAYYIRLMVRDEPGVF 362

Query: 364 AEIAAAMRDAGVSIESLIQRGAMADGSVLVAIVTHEVPERSIAQALEKLRGSPSL 418
           A++A  ++   VS+E +IQRG      V V +  HE  E S+  A++ +R   S+
Sbjct: 363 ADVAGILKAHKVSMEQIIQRGRSPSEVVPVVMTVHETDEASMLGAVKAIRALGSV 417


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: 504
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: 430
Length of database: 428
Length adjustment: 32
Effective length of query: 398
Effective length of database: 396
Effective search space:   157608
Effective search space used:   157608
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.

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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