Alignments for a candidate for aspS2 in Desulfatiglans anilini DSM 4660

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Desulfatiglans anilini DSM 4660

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_035254200.1 H567_RS0111555 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit C

Query= BRENDA::O32038
         (592 letters)



>NCBI__GCF_000422285.1:WP_035254200.1
          Length = 717

 Score =  536 bits (1382), Expect = e-157
 Identities = 286/601 (47%), Positives = 386/601 (64%), Gaps = 30/601 (4%)

Query: 7   YCGDITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALAIAEGI 66
           YCGD++ K  G +V L GWV   RD G L+FI LRD  GIVQVVFNP    +    A  +
Sbjct: 8   YCGDVSGKQAGAAVVLMGWVDAIRDHGNLLFIHLRDIRGIVQVVFNPQTGADLYLEATRL 67

Query: 67  RNEYVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQA------- 119
           + EYV++I+G V  RE GT NPNL TG +E+ A  + +   ++T PF IS++A       
Sbjct: 68  KEEYVVEIEGVVHLREPGTENPNLATGRVEVFASRLRLFARSRTLPFQISEKAMVFGEEL 127

Query: 120 ----EEVSEDVRLKHRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGST 175
               E V E++RL++RYLDLRRP +      R+ + +++R FLDE GF++IETP LT ST
Sbjct: 128 KSSPESVDEELRLQYRYLDLRRPTVQARFVKRYQIIRSIRDFLDERGFVEIETPFLTRST 187

Query: 176 PEGARDYLVPSRVHEGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEF 235
           PEGARD+LVPSR H+G+FYALPQSPQLFKQLLMV G++RY+QIARCFRDEDLR +RQPEF
Sbjct: 188 PEGARDFLVPSRTHQGKFYALPQSPQLFKQLLMVGGMDRYFQIARCFRDEDLRPNRQPEF 247

Query: 236 TQIDIEMSFMSQEDIMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRF 295
           TQ+D+E SF+ +E I  + EE+  ++     G +L  P PRMTY EAM++YGSD+PD RF
Sbjct: 248 TQLDLEASFIDEEFIYEMLEELTCRIF-AVGGIDLPRPFPRMTYAEAMSRYGSDRPDLRF 306

Query: 296 DMLLTDVSDIVKDTEFKVFSSAVANGGVVKAINVKGGAGDYSRKDID---ALGAFAANYG 352
           DM   D++D+ + T + +F      GG++K   VKG A   S+  +    AL    A +G
Sbjct: 307 DMAFEDLTDLFEGTGYAIFRRIRDEGGLIKGFCVKGAADLLSKNILQNEYALKLVPA-FG 365

Query: 353 AKGLAWVKVEADGVKGPIAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAAS-LGAL 411
            KG+ W+KV    ++  I +FF  E+Q+ L+    A EGD+L+  AD    +A   L +L
Sbjct: 366 GKGMTWMKVAGGRLESNIVQFFSPEEQAGLVARFQAGEGDVLMLIADTDRDLAHKVLASL 425

Query: 412 RLKLGKERGLIDEKLFNFLWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPED 471
           RL + +    I +  F  LWV D+PL E   +EGR  + HHPFTMP R + +     P D
Sbjct: 426 RLHVAQRLDRIPQDRFRPLWVTDFPLFEW--KEGRLSSQHHPFTMPDRTEFD-----PRD 478

Query: 472 ------MKAQAYDLVLNGYELGGGSIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFE 525
                 + ++AYDLV+NG ELGGGSIRI +  +Q K+F  L  SPEEA  +FGF L A E
Sbjct: 479 VEGCLQLNSRAYDLVMNGEELGGGSIRIHDMAVQRKIFEALELSPEEAEGKFGFFLNALE 538

Query: 526 YGAPPHGGIALGLDRLVMLLAGRTNLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLS 585
           +GAPPH G+ALGLDR++ ++    N+R+ IAFPK  SA C +T AP  V   QL+EL + 
Sbjct: 539 FGAPPHAGLALGLDRVIAMILKEPNIREIIAFPKNRSAFCPLTRAPAGVDPLQLEELGIG 598

Query: 586 I 586
           +
Sbjct: 599 L 599


Lambda     K      H
   0.319    0.137    0.394 

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: 1122
Number of extensions: 58
Number of successful extensions: 7
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: 592
Length of database: 717
Length adjustment: 38
Effective length of query: 554
Effective length of database: 679
Effective search space:   376166
Effective search space used:   376166
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 (21.7 bits)
S2: 54 (25.4 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