Alignments for a candidate for hom in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for hom in Stenotrophomonas chelatiphaga DSM 21508

Align Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplastic; AK-HD 1; AK-HSDH 1; Beta-aspartyl phosphate homoserine 1; EC 2.7.2.4; EC 1.1.1.3 (characterized)
to candidate WP_057507033.1 ABB28_RS02115 diaminopimelate decarboxylase

Query= SwissProt::Q9SA18
         (911 letters)



>NCBI__GCF_001431535.1:WP_057507033.1
          Length = 864

 Score =  176 bits (446), Expect = 6e-48
 Identities = 148/476 (31%), Positives = 231/476 (48%), Gaps = 40/476 (8%)

Query: 82  DSWAVHKFGGTCVGNSERIKDVAAVVVKDDSE---RKLVVVSAMSKVTDMMYDLIHRAES 138
           D W V KFGGT V    R   +  +  K   E   R LVVVSA+S VT+   +L   A+ 
Sbjct: 8   DRWIVLKFGGTSVSRRHRWDTIGKLAKKRAEETGSRVLVVVSALSGVTN---ELTAIADG 64

Query: 139 RDDSYLSALSGVLEKHRATAVDLLDGDELSSFLARLNDDINNLKAMLRAIYIAGHATESF 198
             DS  + ++ ++E+H+A        DEL    A L + +  L+A+L     A    +  
Sbjct: 65  AADSR-ARVAALVERHQAFL------DELELPRAVLGERLAALQALLDDARAAARTLDWQ 117

Query: 199 SDFVVGHGELWSAQMLAAVVRKSGLDCTWMDARDVLVVIPTSSNQ--------VDPDFVE 250
           ++ V+G GEL S+ + AA + ++GLD  WMDAR  L  +P   NQ        V+  +  
Sbjct: 118 AE-VLGQGELLSSSIGAAYLHQNGLDMGWMDARQWLDALPPLPNQSPWSQRLSVNCQWKS 176

Query: 251 SEKRLEKWFTQNSAKIIIATGFIASTPQNIPTTLKRDGSDFSAAIMSALFRSHQLTIWTD 310
            E   ++ F     +++I  GFIA         L R GSD SAA   AL  + ++ IWTD
Sbjct: 177 DEAWAQR-FRAQPTRLLITQGFIARHADGGTAILGRGGSDTSAAYFGALLGASRVEIWTD 235

Query: 311 VDGVYSADPRKVSEAVVLKTLSYQEAWEMSYFGANVLHPRTIIPVMKYDIPIVIRNIFNL 370
           V G++SA+P+ V +A +L  L Y EA E++  GA VLHPR+I P     +P+ I +    
Sbjct: 236 VPGMFSANPKDVPDARLLTRLDYYEAQEIATTGAKVLHPRSIKPCRDAGVPMAILDTERP 295

Query: 371 SAPGTMICRQIDDEDGFKLDAP-VKGFATIDNLALVNVEGTGMAGVPGTASAIFSAVKEV 429
             PGT I       DG     P VK  +  + + LV++EG GM    G  + +F   K+ 
Sbjct: 296 ELPGTSI-------DGSAAPVPGVKAISRRNGIVLVSMEGIGMWQQVGFLADVFGLFKKH 348

Query: 430 GANVIMISQASSEHSVCFAVPEKEVKA-VSEALNSRFRQALAGGRLSQIEIIPNCSILAA 488
           G +V +I  A +  +V     E  V   V  AL++   Q      + +++II  C+ +  
Sbjct: 349 GLSVDLIGSAETNVTVSLDPSENLVNTDVLAALSADLSQ------ICKVKIIVPCAAITL 402

Query: 489 VGQKMASTPGVSATFFNALAKANINIRAIAQGCSEFNITVVVKREDCIRALRAVHS 544
           VG+ M S     +  +    +  +++  I+Q  ++ N+T V+   D    L  +H+
Sbjct: 403 VGRGMRSLLHKLSDVWATFGRERVHM--ISQSSNDLNLTFVIDETDADGLLPILHA 456


Lambda     K      H
   0.319    0.134    0.385 

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: 1505
Number of extensions: 77
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: 1
Length of query: 911
Length of database: 864
Length adjustment: 43
Effective length of query: 868
Effective length of database: 821
Effective search space:   712628
Effective search space used:   712628
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: 56 (26.2 bits)

This GapMind analysis is from Apr 10 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