GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Sphingomonas koreensis DSMZ 15582

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate Ga0059261_0221 Ga0059261_0221 aspartyl-tRNA synthetase, bacterial type

Query= uniprot:A0A0H3C7V8_CAUVN
         (612 letters)



>FitnessBrowser__Korea:Ga0059261_0221
          Length = 598

 Score =  782 bits (2020), Expect = 0.0
 Identities = 400/615 (65%), Positives = 471/615 (76%), Gaps = 29/615 (4%)

Query: 4   MHAYRTHNCGALRASDTGAAVRLSGWIHRKRDHGGLVFIDLRDHYGLTQLVLHPETPGFN 63
           MHAYR+H CG L A+  G  VRLSGWIHRKRDHGG++F+DLRDHYG+TQ+V   ++P   
Sbjct: 1   MHAYRSHTCGQLTAAQVGETVRLSGWIHRKRDHGGVLFVDLRDHYGVTQIVADSDSPALP 60

Query: 64  VVERLRAESVIRVDGEVIARDASVVNPNLPTGEIEIRVSAVEVLSEAAELPLPVFGEPDY 123
           V+E LR ESV+ +DG V AR  + VNPNL TGEIE+    V V S A ELP+PVFG+ +Y
Sbjct: 61  VLEGLRVESVVTIDGVVKARSDATVNPNLSTGEIEVFAKGVTVQSAAQELPMPVFGDAEY 120

Query: 124 PEEIRLKHRYLDLRRETLHKNIVLRSRVIQSIRNRMFAQGFNEFQTPILTASSPEGARDF 183
           PEEIRL++R+LDLRRE LH NI+LRS VI S+R RM  QGF EFQTPILTASSPEGARD+
Sbjct: 121 PEEIRLRNRFLDLRREGLHANIMLRSHVIASLRRRMIDQGFTEFQTPILTASSPEGARDY 180

Query: 184 LVPSRLHPEKFYALPQAPQQFKQLLMVSGFDRYFQIAPCFRDEDLRADRSL-EFYQLDVE 242
           LV SR+HP KFYALPQAPQ FKQLLMV+GFDRYFQIAPCFRDED RADRS  EFYQLD E
Sbjct: 181 LVASRVHPGKFYALPQAPQMFKQLLMVAGFDRYFQIAPCFRDEDARADRSPGEFYQLDFE 240

Query: 243 MSFVTQEDVFAAIEPVMHGVFEEFSN----GKPVSPINGTHTFTNDFGQSFEHKGFERLT 298
           MS+VTQ+DVFAAIEPV+HGVFEEF++    G+ VSP+                  F+R+ 
Sbjct: 241 MSYVTQDDVFAAIEPVLHGVFEEFADWQGKGRTVSPL-----------------PFKRIP 283

Query: 299 YAQSMAWYGSDKPDLRNPIKMANVSEHFRDGGFGLFAKILGADAKNQVWAIPAP--TGGS 356
           Y +SM  YG+DKPDLRNPI +++VS+HF   GFG FA I+  +A + V AIPAP     S
Sbjct: 284 YRESMLKYGNDKPDLRNPILISDVSKHFEGSGFGRFASIV--EAGDVVRAIPAPGTAEKS 341

Query: 357 RAFCDRMNSWAQGEGQPGLGYVFWSEDQGGWGGPIAKNLGE-PTQALMESLGLGAGDAAF 415
           R F D MN+WAQGEG  GLGY   +   G WGGPIAKN GE    AL + LGLG  D  F
Sbjct: 342 RKFFDDMNAWAQGEGFAGLGYA--TRKGGEWGGPIAKNHGEDKMSALADELGLGPDDGIF 399

Query: 416 FVAGDPAVFAKFAGLARTRVGTELKLVDENQFKFCWIVDFPMFEWNEEEKKVDFSHNPFS 475
           F AG  A  AK AGLARTRVG +L+L+D+N+F+FCWIVDFPMFE++E+ KK+DFSHNPFS
Sbjct: 400 FAAGKEAQAAKLAGLARTRVGEQLELIDKNRFEFCWIVDFPMFEYDEDAKKIDFSHNPFS 459

Query: 476 MPQGGLEALETQDPLTIRAYQYDIVCNGYELCSGAIRNHKPEIMLKAFATAGYGPEVVEE 535
           MPQG LEALET+DPL I A+QYDIVCNG EL SGAIRNH+PEIM KAF  AGY  E V+ 
Sbjct: 460 MPQGELEALETKDPLDILAWQYDIVCNGIELSSGAIRNHRPEIMYKAFEIAGYTQEQVDS 519

Query: 536 QFGGMLNAFRYGAPPHGGLAPGIDRIVMLLADQVAIREVIAFPLNQQGQDLLMNAPANVL 595
            F GM+NAF++GAPPHGG APG+DRIVMLLADQ  IREVI FP+NQ+ +DL+M AP+ V 
Sbjct: 520 NFAGMINAFKFGAPPHGGSAPGVDRIVMLLADQPNIREVIVFPMNQKAEDLMMQAPSFVS 579

Query: 596 DKQLKELHIRTAPPI 610
           +KQLKELHIR AP +
Sbjct: 580 EKQLKELHIRLAPGV 594


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: 1127
Number of extensions: 51
Number of successful extensions: 5
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: 598
Length adjustment: 37
Effective length of query: 575
Effective length of database: 561
Effective search space:   322575
Effective search space used:   322575
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

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:

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