Alignments for a candidate for aspS2 in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Escherichia coli BW25113

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate 18157 b4129 lysine tRNA synthetase, inducible (NCBI)

Query= curated2:B2V713
         (602 letters)



>FitnessBrowser__Keio:18157
          Length = 505

 Score =  130 bits (327), Expect = 1e-34
 Identities = 110/350 (31%), Positives = 174/350 (49%), Gaps = 47/350 (13%)

Query: 7   EFKRDYYCGDLNES----------NIGDEVRLLGWVDTVRDHGGVIFINLRDREGIVQVV 56
           +F+RD+    L+E           ++  EV + G + T R  G   F+ L+D  G +Q+ 
Sbjct: 39  DFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLY 98

Query: 57  FDPSKIGEELYN-KAKKLKSEYVIGVRGRVYRRPAGTENPKMKTGNIEVAGEELLILNTS 115
                + E +YN + KK     +IG RG ++         K +TG + +   EL +L  +
Sbjct: 99  VARDSLPEGVYNDQFKKWDLGDIIGARGTLF---------KTQTGELSIHCTELRLL--T 147

Query: 116 KAL-PFPIEDNIKVSEEVRLKYRYLDL-RRPSMQRNIILRHEVYQAVREFLAGNGFIEVE 173
           KAL P P + +    +EVR + RYLDL      ++  ++R ++  A+R+F+   GF+EVE
Sbjct: 148 KALRPLPDKFHGLQDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVARGFMEVE 207

Query: 174 TPMLTKSTPEGA--RDFLVPSRLEKGKFYALPQSPQLFKQILMVAGLERYFQIAKCFRDE 231
           TPM+ +  P GA  R F+          Y L  +P+L+ + L+V G ER F+I + FR+E
Sbjct: 208 TPMM-QVIPGGASARPFITHHNALDLDMY-LRIAPELYLKRLVVGGFERVFEINRNFRNE 265

Query: 232 DLRADRQPEFTQIDLEMSFVTEDDVMTLAESLIQYVYKKVLG----------IDIKIPFR 281
            +     PEFT ++L M++    D++ L ESL + + ++VLG           D   PF 
Sbjct: 266 GISVRHNPEFTMMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFE 325

Query: 282 RMSYEEAINKY--GTDKPDLRYGLELIDITDLAKEVEFKVFNDVAKSGGL 329
           +++  EAI KY   TD  DL       D  D AK +   +   V KS GL
Sbjct: 326 KLTMREAIKKYRPETDMADL-------DNFDAAKALAESIGITVEKSWGL 368



 Score = 54.3 bits (129), Expect = 1e-11
 Identities = 31/86 (36%), Positives = 44/86 (51%), Gaps = 4/86 (4%)

Query: 488 YDMVLNGEEIGGGSIRIHTPYIQEKVFQ----LLNISEEEAKEKFGFLIEALSYGAPPHG 543
           ++  + G EIG G   ++    Q + FQ         ++EA       + AL YG PP  
Sbjct: 414 FEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAGDDEAMFYDEDYVTALEYGLPPTA 473

Query: 544 GLAFGLDRILALMTGSESIRDVIAFP 569
           GL  G+DR++ L T S +IRDVI FP
Sbjct: 474 GLGIGIDRMIMLFTNSHTIRDVILFP 499


Lambda     K      H
   0.319    0.140    0.399 

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: 687
Number of extensions: 40
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 602
Length of database: 505
Length adjustment: 36
Effective length of query: 566
Effective length of database: 469
Effective search space:   265454
Effective search space used:   265454
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 Apr 09 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