Alignments for a candidate for aspS2 in Hyphomicrobium sulfonivorans WDL6

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Hyphomicrobium sulfonivorans WDL6

Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_068460798.1 APY04_RS06185 aspartate--tRNA ligase

Query= reanno::Caulo:CCNA_01969
         (612 letters)



>NCBI__GCF_001541235.1:WP_068460798.1
          Length = 601

 Score =  785 bits (2027), Expect = 0.0
 Identities = 392/615 (63%), Positives = 472/615 (76%), Gaps = 24/615 (3%)

Query: 4   MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63
           MH YR+H CGALRASD G  VRLSGW+HR RDHGG++FIDLRDHYG+TQ+V  P++P F 
Sbjct: 1   MHRYRSHTCGALRASDIGNTVRLSGWVHRVRDHGGVLFIDLRDHYGITQVVADPDSPAFK 60

Query: 64  VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123
             E +R+E VIR+DG V  R     N +LPTGEIE+  + +EVLS+A ELP+PVFGEPDY
Sbjct: 61  NAEAVRSEWVIRIDGTVRKRPDGTTNADLPTGEIELFATEIEVLSQAKELPVPVFGEPDY 120

Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183
           PE++RL++R+LDLRRETLH+NI+ R  +I S+R RM   GF EF TPILTASSPEGARDF
Sbjct: 121 PEDLRLQYRFLDLRRETLHRNIMQRMAIIASLRKRMTEGGFFEFSTPILTASSPEGARDF 180

Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADR-SLEFYQLDVE 242
           LVPSR+H  KFYALPQAPQQ+KQLLMVSGFDRYFQIAPCFRDED RADR   EFYQLDVE
Sbjct: 181 LVPSRIHAGKFYALPQAPQQYKQLLMVSGFDRYFQIAPCFRDEDPRADRLPGEFYQLDVE 240

Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSNGKPVSPINGTH-TFTNDFGQSFEHKGFERLTYAQ 301
           MSFVTQ+DVF  +EPV+ GVFEEF      S I G+  + TN         G+ R+ Y++
Sbjct: 241 MSFVTQDDVFNEMEPVITGVFEEF------SAITGSEKSVTN---------GWPRIPYSE 285

Query: 302 SMAWYGSDKPDLRNPIKMANVSEHFRDGGFGLFAKILGADAKNQVWAIPAPTGGSRAFCD 361
           ++A YGSDKPDLRNPI+M +V+EHFR  GF +FA ++  D K +VWAIPAP GGSRAFCD
Sbjct: 286 AIAKYGSDKPDLRNPIEMQDVTEHFRGSGFKIFAGMIDKDPKVRVWAIPAPGGGSRAFCD 345

Query: 362 RMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLG-EPTQALMESLGLGAGDAAFFVAGD 420
           RMNSWAQGEGQPGL Y+F+ E  G   GP+ KNLG E   A+ E +GL  GDA FF AG+
Sbjct: 346 RMNSWAQGEGQPGLAYIFFRE--GEAAGPVGKNLGPERADAIREQMGLKEGDAVFFTAGN 403

Query: 421 PAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFSMPQGG 480
           PA F +FAG ARTR+G ELKL+DE++F   WIVDFP +EWN+++KK+DFSHNPFSMPQGG
Sbjct: 404 PARFHRFAGDARTRIGEELKLIDESKFALAWIVDFPFYEWNDDDKKIDFSHNPFSMPQGG 463

Query: 481 LEALE----TQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEEQ 536
           LEALE      + L I+AYQYDIVCNG+E+ SG+IRNH+P+ M+KAF   G     VE +
Sbjct: 464 LEALEGAASDDERLNIKAYQYDIVCNGFEIASGSIRNHRPDTMVKAFEITGLTQADVEAR 523

Query: 537 FGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVLD 596
           FGG+  AF+YGAPPHGG+A GIDRIVMLL     +RE+  FP+NQQ  DLLM AP++V  
Sbjct: 524 FGGLYRAFQYGAPPHGGMAAGIDRIVMLLVGAKNLREISLFPMNQQANDLLMGAPSDVAP 583

Query: 597 KQLKELHIRTAPPIK 611
           KQL+ELHIR   P K
Sbjct: 584 KQLRELHIRVVAPEK 598


Lambda     K      H
   0.321    0.139    0.425 

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: 1176
Number of extensions: 47
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: 612
Length of database: 601
Length adjustment: 37
Effective length of query: 575
Effective length of database: 564
Effective search space:   324300
Effective search space used:   324300
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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