Alignments for a candidate for hom in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Pyrolobus fumarii 1A

Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_014026853.1 PYRFU_RS06440 aspartate kinase

Query= reanno::Cola:Echvi_2000
         (815 letters)



>NCBI__GCF_000223395.1:WP_014026853.1
          Length = 480

 Score =  205 bits (521), Expect = 5e-57
 Identities = 139/459 (30%), Positives = 238/459 (51%), Gaps = 18/459 (3%)

Query: 3   IIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEESYH 62
           + KFGGS + + E+  +   I E+   + +  LV SA  GVT++LL+   +A+  E S  
Sbjct: 19  VAKFGGSVLKSGEDYARAAEITEELQREHSVILVVSAMKGVTDRLLR---LARDFEASPS 75

Query: 63  TILQELEKRHLEIVKKL-VPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYVL 121
             + EL + H+E ++   V  +    A + +    +EL  +   + ++ E + + +DYV+
Sbjct: 76  VEIPELYQMHVEALRGAGVSGRLFGEAFSRIARLIDELTKIIWALRVLGEVTPKALDYVV 135

Query: 122 SFGERLSNFILAAGLQAKGIGTSYVDARDL-VKTDDRFGHAKVNFKTTNKLIQDHFKSHD 180
           SFGERLS  I+ A L+++GI    +   +  + TDDRFG A    + T   ++       
Sbjct: 136 SFGERLSAVIMEAVLRSRGIEAKALTGWEAGIVTDDRFGEANPIMEETVPRVRSRLLPLT 195

Query: 181 D---IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRL 237
           +   + ++TGFI +T KG+ TT+GR GSDYTAS+ A+ LGA +V  +TDV GVMTADPRL
Sbjct: 196 EKGIVPIVTGFIAATRKGDITTLGRGGSDYTASLIASILGATEVHFYTDVPGVMTADPRL 255

Query: 238 VYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS 297
           +  A TIP+L   EA+ELS  G K   P T +P +   I   I +   P    T +  + 
Sbjct: 256 IPEARTIPRLCVIEALELSRVGGKKFHPRTFEPLLYSKIRARILDAKDPHGPHTIVEPEC 315

Query: 298 GEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICV 357
            +   +K ++ M  ++++ ++G  +   +G +          G+NI+ ISQ  +E  I +
Sbjct: 316 ID--TLKAVAVMRGLAVVRLEGAVMAGRIGTAMMVTSVSKRAGVNIVAISQPVTETRIEI 373

Query: 358 AIASKDASRAKSVIEEEFRYEIQSGEMD-EIQIVPDMAVIAVVGENMQHNPGASGRMF-Q 415
            +A +DA R    + EE R +    E+D  + +   ++ + +VG  ++ NP    R+  +
Sbjct: 374 VVAEEDAERLAKALSEEIRNQ----ELDVNVMVETGLSAVTIVGYGLR-NPSLRARVLSE 428

Query: 416 ALG-RNNVNVAAIAQGSSELNISAVITQADLQKALNALH 453
           AL       + +I  G  + +++ V    D  +    +H
Sbjct: 429 ALSLEPEPELRSITTGFHDASLTIVTNARDAVRIAERIH 467



 Score = 34.3 bits (77), Expect = 2e-05
 Identities = 29/140 (20%), Positives = 61/140 (43%), Gaps = 13/140 (9%)

Query: 361 SKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALGRN 420
           +KD     +++E E    +++     + ++  +AV+ + G  M    G +  +     R 
Sbjct: 301 AKDPHGPHTIVEPECIDTLKA-----VAVMRGLAVVRLEGAVMAGRIGTAMMVTSVSKRA 355

Query: 421 NVNVAAIAQGSSELNISAVITQADLQKALNALHEAF--------FLSDYKVLHLFLVGVG 472
            VN+ AI+Q  +E  I  V+ + D ++   AL E           + +  +  + +VG G
Sbjct: 356 GVNIVAISQPVTETRIEIVVAEEDAERLAKALSEEIRNQELDVNVMVETGLSAVTIVGYG 415

Query: 473 LIGKALTKMIHQQLKNLQEE 492
           L   +L   +  +  +L+ E
Sbjct: 416 LRNPSLRARVLSEALSLEPE 435


Lambda     K      H
   0.317    0.134    0.375 

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: 739
Number of extensions: 36
Number of successful extensions: 5
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: 815
Length of database: 480
Length adjustment: 37
Effective length of query: 778
Effective length of database: 443
Effective search space:   344654
Effective search space used:   344654
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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 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 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