Alignments for a candidate for aspS2 in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Chlorobaculum parvum NCIB 8327

Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_012502576.1 CPAR_RS06800 aspartate--tRNA(Asp/Asn) ligase

Query= reanno::Dino:3609247
         (590 letters)



>NCBI__GCF_000020505.1:WP_012502576.1
          Length = 603

 Score =  612 bits (1577), Expect = e-179
 Identities = 317/593 (53%), Positives = 412/593 (69%), Gaps = 12/593 (2%)

Query: 4   FRTHTCAELTKDAVGQTVRLSGWVHRVRDHGGVLFIDLRDHYGMTQVLCDPDS-PVFSQV 62
           FRTH C  L +D+ G  V+L GWVHR+RDHGG++FIDLRDH G+ Q++  P+S  +F   
Sbjct: 15  FRTHYCGLLNRDSEGAGVKLGGWVHRIRDHGGLIFIDLRDHTGICQLVIQPESGELFRIA 74

Query: 63  EKVRSEWCIRIDGTVKARDESLINPKIPTGEIEVFIRDMEVLGTAEELPLPVFGDQEYPE 122
           E + SE  I  +G+V  R +  +NP++ +G IEV +  +++   A  LP PV       E
Sbjct: 75  EGLHSESVISAEGSVVLRSDETVNPRLASGAIEVVVSAIKIESAAHPLPFPVADYMPTSE 134

Query: 123 ETRLKYRFLDLRRESLHDNIMLRSKVVQSIRKRMWDIDFTEFQTPIITASSPEGARDFLV 182
           E RLKYRFLDLRRE LH+NI+ RS++  ++RK + D+DF E QTPI+T+SSPEGARDFLV
Sbjct: 135 ELRLKYRFLDLRRERLHENIIFRSQLTAAVRKYLTDLDFIEIQTPILTSSSPEGARDFLV 194

Query: 183 PSRLHPGKFYALPQAPQQFKQLIMVGGFDKYFQIAPCFRDEDPRADRSPTDFYQLDLEMS 242
           PSRLHPGKFYALPQAPQQFKQL+MV GF +YFQIAPCFRDED RADRSP +FYQ+D+EMS
Sbjct: 195 PSRLHPGKFYALPQAPQQFKQLLMVSGFPRYFQIAPCFRDEDARADRSPGEFYQVDIEMS 254

Query: 243 FVSQQDVFDTIQPVIAGIFEEFGGGRRVDTDWPLISYRDSALWYGTDKPDLRNPIKMQIV 302
           FV Q D+F  ++ +   + E     R     +P ISY+D    YG+DKPDLR PI++Q V
Sbjct: 255 FVEQDDLFVILEGMFKHLVETMTTKRIAQYPFPRISYKDVMNRYGSDKPDLRIPIEIQDV 314

Query: 303 SDHFAGSGFAIFAKLLEQEGTEIRAIPAPGGG--SRKFCDRMNKFAQEQGLPGMGYIFWR 360
           ++ F  SGF +FA    +EG  ++A+   G G  SR F D+  K A+E G  G+ YI ++
Sbjct: 315 TELFVNSGFKVFAS-NTKEGCCVKAMVLKGMGNESRLFYDKAEKRARELGSAGLAYIQFK 373

Query: 361 DQGQGMEAAGPLAKNIGPERTEAIRQQLGLQVGDAAFFLGGKPASFEAVAGRARTVIGEE 420
           ++       GP+ K +  E   A+++QLG++ GD  FF  GK      + G  R    + 
Sbjct: 374 EEA----PKGPVVKFLKEEEMAALKEQLGIETGDVVFFGAGKWEQTCKIMGGMRNYFADV 429

Query: 421 LGLIDQDRFAFAWIVDFPMYEKDDEG-RIDFSHNPFSMPQGGMAALE-GDPLEVLGYQYD 478
             L D+D  +F WIVDFPM+E ++E  +IDFSHNPFSMPQG M ALE   PL++L YQYD
Sbjct: 430 FPL-DRDELSFCWIVDFPMFEYNEEDKKIDFSHNPFSMPQGEMEALEQHSPLDILAYQYD 488

Query: 479 LACNGYELVSGAIRNHKLDIMYKAFEIAGYGADEVEKRFGGMVNAFKYGPPPHGGCAAGI 538
           + CNG EL SGAIRNH+ DIMYKAFEIAGY  DEV+ RFG M+ AFK+G PPHGG A G+
Sbjct: 489 IVCNGIELSSGAIRNHRPDIMYKAFEIAGYPHDEVDARFGHMIEAFKHGAPPHGGIAPGL 548

Query: 539 DRIVMLLADTANIREVIMFPMNQRAEDLMMNAPSEPTGEQLRDLSLRV-IPQE 590
           DR+VM+L D  NIREVI FPMNQ A+DLMM APSE T +QL++L ++V +P+E
Sbjct: 549 DRLVMILRDEQNIREVIAFPMNQSAQDLMMAAPSEVTAQQLKELHIKVELPEE 601


Lambda     K      H
   0.322    0.141    0.431 

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: 1051
Number of extensions: 46
Number of successful extensions: 6
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: 590
Length of database: 603
Length adjustment: 37
Effective length of query: 553
Effective length of database: 566
Effective search space:   312998
Effective search space used:   312998
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 (21.9 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