Alignments for a candidate for asd-S-transferase in Methanococcus aeolicus Nankai-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd-S-transferase in Methanococcus aeolicus Nankai-3

Align L-aspartate semialdehyde sulfurtransferase (EC 2.8.1.16) (characterized)
to candidate WP_011973508.1 MAEO_RS03970 CBS domain-containing protein

Query= BRENDA::Q57564
         (509 letters)



>NCBI__GCF_000017185.1:WP_011973508.1
          Length = 511

 Score =  726 bits (1875), Expect = 0.0
 Identities = 351/506 (69%), Positives = 430/506 (84%), Gaps = 2/506 (0%)

Query: 3   MKTIKEINEKIKKGEAVVVTAEEMIKIVEEEGAKRAADYVDVVTTGTFGAMCSSGVFINF 62
           MKTI EINEKIK  +AVVV AEEMIKIVE+ G+K A+  VD+VTTGTFGAMCSSG+F+NF
Sbjct: 1   MKTIAEINEKIKNNDAVVVNAEEMIKIVEDIGSKNASKEVDIVTTGTFGAMCSSGIFLNF 60

Query: 63  GHSDPPIKMLRIYLNNVEAYGGLAAVDAYIGAAQPNEDPDVDIDYGGAHVIEDLVRGKEV 122
           GHSDPPIKM++ YLN VEAY G+AAVDAY+GA QPN D D+DI+YGGAHVIEDLV  KE+
Sbjct: 61  GHSDPPIKMIKTYLNGVEAYSGVAAVDAYLGATQPNSDDDIDINYGGAHVIEDLVAKKEI 120

Query: 123 ELYAEGYTTDCYPRKEVNVRITLDDVNQAIMVNPRNCYQTYAAATNSREEKIYTYMGILL 182
            L AEGYTTDCYPRK+V+  IT+DD+NQAIM+NPRNCYQ+Y AATNS +EK+YTYMG LL
Sbjct: 121 TLKAEGYTTDCYPRKKVSTTITIDDLNQAIMINPRNCYQSYVAATNSLDEKLYTYMGTLL 180

Query: 183 PEYNNVHYSGAGQLNPLQNDYNPETKSFNTIGIGTRIFLGGGIGYVIGEGTQHNP--PFG 240
           PE  N++YSGAGQLNPLQNDYN  TKS+NTIGIGT+IFLGG  GY+IGEGTQH+P   FG
Sbjct: 181 PELGNINYSGAGQLNPLQNDYNNTTKSYNTIGIGTKIFLGGAEGYIIGEGTQHSPDTKFG 240

Query: 241 TLMVKGDLKQMNPKFIRAATMPRYGSTLYVGIGIPIPVLNEKIAERCAIRDEDIEVPIYD 300
           T+M+KGDLK+M+ K+IRA+T+P+YG +L+VG+G+PIPVLNE++A+ CAIRDEDIE+PI D
Sbjct: 241 TIMIKGDLKEMDKKYIRASTIPKYGPSLFVGMGVPIPVLNEEVAKSCAIRDEDIEIPILD 300

Query: 301 YGFPRRDRPLIAKTNYKVLRSGKITLNVNIDGKDVEKTVKTGSVSSYKMAREVAETLKQW 360
           YG  RRDRP+I KTNYK LR+G+IT  +NIDG+ +E+T+KT SVSSYK +RE+AE LK+W
Sbjct: 301 YGVQRRDRPVIGKTNYKELRTGEITTKLNIDGEIIEETIKTASVSSYKKSREIAEELKKW 360

Query: 361 ILDGKFLLTERVDTLGRAENKPMKSPITLVKDILSKPPITAHSNISIMEAAKILIKHNIN 420
           IL G FLLTERV+ L  A  KPMK+   LV DI+SKPPI A+ NISI EA+KILI++ IN
Sbjct: 361 ILKGDFLLTERVNPLSYAAPKPMKAQAKLVGDIISKPPILANQNISINEASKILIENGIN 420

Query: 421 HLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNI 480
           HLPIVDE+  LVGIITSWDIA+A+AQNK +I EIMT  VI++  DEP+D +A KMS YNI
Sbjct: 421 HLPIVDENKNLVGIITSWDIARAVAQNKNSILEIMTATVISSTVDEPIDVLARKMSIYNI 480

Query: 481 SGVPVVDDYRRVVGIVTSEDISRLFG 506
           SG P++D  ++VVG++T+ED+S+L G
Sbjct: 481 SGAPILDKNKKVVGMITAEDLSKLVG 506


Lambda     K      H
   0.317    0.137    0.393 

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: 868
Number of extensions: 42
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 509
Length of database: 511
Length adjustment: 34
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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: 52 (24.6 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