GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Salinicoccus carnicancri Crm

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_017548732.1 C792_RS0106905 aspartate--tRNA ligase

Query= BRENDA::O32038
         (592 letters)



>NCBI__GCF_000330705.1:WP_017548732.1
          Length = 585

 Score =  758 bits (1956), Expect = 0.0
 Identities = 373/577 (64%), Positives = 454/577 (78%), Gaps = 2/577 (0%)

Query: 10  DITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALAIAEGIRNE 69
           ++TE   GE VTLKGWVQKRRDLGGLIFIDLRDR G++QVVFNP++SKEAL  AE IR+E
Sbjct: 7   EVTESQTGEKVTLKGWVQKRRDLGGLIFIDLRDRKGVIQVVFNPEISKEALETAERIRSE 66

Query: 70  YVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEEVSEDVRLK 129
           YV+++ G+V+ R+   VN N+ TG IEI AD V VL+ A+TPPF I D  + + EDVRLK
Sbjct: 67  YVIEVSGEVLKRDPSQVNENIATGKIEILADEVTVLSKAETPPFQILD--DSIGEDVRLK 124

Query: 130 HRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARDYLVPSRVH 189
           +RY DLRR  +  T++LRH + ++VR+FLD   F+DIETP+L+ STPEGARDYLVPSRVH
Sbjct: 125 YRYFDLRRNKLQNTLRLRHQINRSVRNFLDNEEFVDIETPVLSKSTPEGARDYLVPSRVH 184

Query: 190 EGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIEMSFMSQED 249
           EGEFYALPQSPQ++KQLLM+SG+E+YYQI +CFRDEDLRADRQPEFTQIDIEMSFM QE 
Sbjct: 185 EGEFYALPQSPQIYKQLLMLSGMEKYYQIVKCFRDEDLRADRQPEFTQIDIEMSFMDQEQ 244

Query: 250 IMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTDVSDIVKDT 309
           IM L E ++  VM+  KG ++ LP+PRMTY++AM +YG DKPDTRF + L D+S+  +  
Sbjct: 245 IMELNERLIRHVMKTVKGVDIALPIPRMTYEQAMAEYGIDKPDTRFGLKLNDLSEFSRTV 304

Query: 310 EFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKVEADGVKGP 369
           +FKVF S V NGG+VKAI VKG A  +SRKDID L A+   YGAKGLAW+KV+   + GP
Sbjct: 305 DFKVFRSTVENGGMVKAIVVKGEADSFSRKDIDKLEAYVKTYGAKGLAWLKVKDGALNGP 364

Query: 370 IAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGLIDEKLFNF 429
           IAKFF+E+ Q +L E L   +GDL LF AD  +VV ASLG LR KL K+  LI+   +NF
Sbjct: 365 IAKFFNEDNQKELSETLGLEDGDLTLFVADSAKVVHASLGNLRNKLAKDLDLIEADQYNF 424

Query: 430 LWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVLNGYELGGG 489
           LWV DWPL E+D E GR++AAHHPFT P  ED+EL+ET PE +KA AYD+VLNGYELGGG
Sbjct: 425 LWVTDWPLFEYDEEAGRYFAAHHPFTSPKAEDVELLETEPEKVKANAYDIVLNGYELGGG 484

Query: 490 SIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRLVMLLAGRT 549
           SIRI +  +Q+KMF  LGF+ EE  EQFGFL+EAF+YGAPPHGGIA GLDRLVMLLAG  
Sbjct: 485 SIRIHDAQMQQKMFRALGFTDEERDEQFGFLIEAFKYGAPPHGGIAYGLDRLVMLLAGTD 544

Query: 550 NLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLSI 586
           N+RD IAFPKTASA+ LM  AP EV+ AQL ELH+ +
Sbjct: 545 NIRDVIAFPKTASAADLMMSAPSEVAKAQLKELHIEL 581


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: 965
Number of extensions: 34
Number of successful extensions: 2
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: 585
Length adjustment: 37
Effective length of query: 555
Effective length of database: 548
Effective search space:   304140
Effective search space used:   304140
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: 53 (25.0 bits)

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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