Alignments for a candidate for hom in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Roseburia faecis M72

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055068006.1 M72_RS09220 aspartate kinase

Query= reanno::Btheta:351931
         (811 letters)



>NCBI__GCF_001406815.1:WP_055068006.1
          Length = 439

 Score =  164 bits (416), Expect = 7e-45
 Identities = 136/462 (29%), Positives = 213/462 (46%), Gaps = 37/462 (8%)

Query: 1   MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGG-------ITDKLINTSKMAA 53
           +KV+KFGG+S+ S      V  I+ +      VV SA G        +TD L      A 
Sbjct: 2   VKVVKFGGSSLASAEQFAKVGDIIRADESRKYVVPSAPGKRNSRDTKVTDMLYACYAKAE 61

Query: 54  AGDSAYEGEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSP 113
           AG+     EFR  + +  E    +I     +V L  +   +    K+   G+        
Sbjct: 62  AGE-----EFRVPLMKIKERYDSIINGLGLKVTLDEEFKTISKNFKEK-AGV-------- 107

Query: 114 KTSDTIVSYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHS 173
              D   S GE L+ I++A+ +   ++ DS T I  +++ N   +DAD T++++ +    
Sbjct: 108 ---DYAASRGEYLNGILMADYLGY-EFIDSATVIFFDEEGN---LDADKTDKVLAKKLSE 160

Query: 174 IPKVSLVPGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRV 233
             K +++PGF       G V    RGGSD T +I+A A  AS  E WTDV G + ADPR+
Sbjct: 161 CEK-AVIPGFYGIG-ADGRVKTFSRGGSDITGSIVAKACHASLYENWTDVSGCLVADPRI 218

Query: 234 ISTAYTISELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQET 293
           I     I  ++Y E  EL   GA V++   ++PV    IPI I+NT +P+  GT+I + T
Sbjct: 219 IDNPQPIHVITYRELRELSYMGASVLHEDAVFPVRKAGIPINIRNTNDPEAEGTLIVEST 278

Query: 294 SNPQSKAIKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENST 353
                  I GI+       +++    M   +G   +  +A  +NGIS+      S  ++ 
Sbjct: 279 CQKPEYTITGIAGKKGFVAVSIDKDMMNSEVGFCRKALQAFEENGISI--EHMPSGIDTM 336

Query: 354 SIGVRNADADLACEVLNEEFAKEI-EMGEISPILAERNLATVAIVGENMKHTPGIAGKLF 412
           ++ V   +     E   ++    I  +     I  E +L  +A+VG  MK T G AG++F
Sbjct: 337 TVFVHQEE----FEGKEQQVISSIRRLTHPDVIDLEADLGLIAVVGRGMKSTRGTAGRIF 392

Query: 413 GTLGRNGINVIACAQGASETNISFVVDSKSLRKSLNVIHDSF 454
             L    INV    QG+SE NI   V +     ++  I+D F
Sbjct: 393 SALAHANINVKMIDQGSSELNIIIGVSNDDFEAAIKAIYDIF 434



 Score = 46.2 bits (108), Expect = 4e-09
 Identities = 34/107 (31%), Positives = 49/107 (45%), Gaps = 13/107 (12%)

Query: 282 PDGVGT----VIKQETSNPQSKAIKGISSIN---------DTSLITVQGLGMVGVIGVNY 328
           P G+ T    V ++E    + + I  I  +          D  LI V G GM    G   
Sbjct: 330 PSGIDTMTVFVHQEEFEGKEQQVISSIRRLTHPDVIDLEADLGLIAVVGRGMKSTRGTAG 389

Query: 329 RIFKALAKNGISVFLVSQASSENSTSIGVRNADADLACEVLNEEFAK 375
           RIF ALA   I+V ++ Q SSE +  IGV N D + A + + + F +
Sbjct: 390 RIFSALAHANINVKMIDQGSSELNIIIGVSNDDFEAAIKAIYDIFVE 436


Lambda     K      H
   0.317    0.135    0.377 

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: 722
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 811
Length of database: 439
Length adjustment: 37
Effective length of query: 774
Effective length of database: 402
Effective search space:   311148
Effective search space used:   311148
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Jul 25 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis