Alignments for a candidate for aspS2 in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Teredinibacter turnerae T7901

Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_015817601.1 TERTU_RS03770 aspartate--tRNA ligase

Query= SwissProt::Q51422
         (591 letters)



>NCBI__GCF_000023025.1:WP_015817601.1
          Length = 600

 Score =  852 bits (2202), Expect = 0.0
 Identities = 405/589 (68%), Positives = 488/589 (82%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MRS YCG L  +  G+EVTLCGWV RRRDHGGVIF+D+RDR+G+ QVVFDPD  + FA A
Sbjct: 1   MRSVYCGVLTAANIGEEVTLCGWVDRRRDHGGVIFVDLRDRDGIVQVVFDPDAEDNFALA 60

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           D+VR E+V+++TGKVR R E   N NMA+G +E+ G  L +LN A+TPPF LD ++ VGE
Sbjct: 61  DKVRPEYVLQVTGKVRARSESTVNANMATGEVEIYGTGLTILNTADTPPFQLDSFTSVGE 120

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
           + RLRYR++DLRR EM   L+ R+++T++IR YLD++GFLD+ETPIL R TPEGARDYLV
Sbjct: 121 DVRLRYRYLDLRRKEMQHNLRFRSKVTNAIRNYLDEHGFLDIETPILTRATPEGARDYLV 180

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSRT+   FFALPQSPQLFKQLLMV+GFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF
Sbjct: 181 PSRTHESKFFALPQSPQLFKQLLMVSGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 240

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301
           +DE  I+ +TE M+R+LF +VL ++  +FP MP+ EAM +YGSDKPD+RIPLE+V++ D 
Sbjct: 241 MDEEQIMSVTEGMIRKLFNDVLSIDLGDFPRMPYSEAMEKYGSDKPDMRIPLEMVEIKDL 300

Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361
           +K+VEFKVFS PANDPK RV A+RVP    +PR +ID YTKFV IYGAKGLAYIKVN++ 
Sbjct: 301 MKDVEFKVFSAPANDPKSRVTAMRVPQGGEIPRKKIDAYTKFVSIYGAKGLAYIKVNDKD 360

Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDLK 421
               GLQSPIVKF+P      IL+RVGA +GD++FFGAD  K+V +ALGALR K+G DL 
Sbjct: 361 DLENGLQSPIVKFLPAEVCKAILERVGAENGDLIFFGADTTKVVTEALGALRCKLGEDLD 420

Query: 422 LLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLNG 481
           L T EWAP+WVVDFPMFEE D+G L+ALHHPFT+P C+P +L+ANP  ALSRAYDMVLNG
Sbjct: 421 LYTCEWAPLWVVDFPMFEETDEGGLTALHHPFTAPSCSPEDLQANPATALSRAYDMVLNG 480

Query: 482 TELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLVM 541
           TELGGGS+RIH++ MQQAVF++LGI   EQ EKFGFLLDALK+GAPPHGGLAFGLDRL+M
Sbjct: 481 TELGGGSVRIHNQDMQQAVFKILGISPEEQREKFGFLLDALKFGAPPHGGLAFGLDRLIM 540

Query: 542 LMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKA 590
           LMTGA SIR+VIAFPKTQSA  +MT APG+VD K L+ELHIRLR +P+A
Sbjct: 541 LMTGADSIRDVIAFPKTQSAACLMTDAPGAVDAKQLQELHIRLRAKPQA 589


Lambda     K      H
   0.321    0.140    0.411 

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: 1120
Number of extensions: 35
Number of successful extensions: 1
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: 591
Length of database: 600
Length adjustment: 37
Effective length of query: 554
Effective length of database: 563
Effective search space:   311902
Effective search space used:   311902
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: 53 (25.0 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